tjh.dev
1{ lib
2, fetchPypi
3, rPackages
4, rWrapper
5, buildPythonPackage
6, biopython
7, numpy
8, scipy
9, scikitlearn
10, pandas
11, matplotlib
12, reportlab
13, pysam
14, future
15, pillow
16, pomegranate
17, pyfaidx
18}:
19
20buildPythonPackage rec {
21 pname = "CNVkit";
22 version = "0.9.7";
23
24 src = fetchPypi {
25 inherit pname version;
26 sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a";
27 };
28
29 propagatedBuildInputs = [
30 biopython
31 numpy
32 scipy
33 scikitlearn
34 pandas
35 matplotlib
36 reportlab
37 pyfaidx
38 pysam
39 future
40 pillow
41 pomegranate
42 ];
43
44 postPatch = ''
45 substituteInPlace setup.py \
46 --replace "pandas >= 0.20.1, < 0.25.0" "pandas"
47 '';
48
49 pythonImportsCheck = [ "cnvlib" ];
50
51 meta = with lib; {
52 homepage = "https://cnvkit.readthedocs.io";
53 description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
54 license = licenses.asl20;
55 maintainers = [ maintainers.jbedo ];
56 };
57}