tjh.dev
1{ lib
2, fetchPypi
3, rPackages
4, rWrapper
5, buildPythonPackage
6, biopython
7, numpy
8, scipy
9, pandas
10, matplotlib
11, reportlab
12, pysam
13, future
14, pillow
15, pomegranate
16, pyfaidx
17}:
18
19buildPythonPackage rec {
20 pname = "CNVkit";
21 version = "0.9.6";
22
23 src = fetchPypi {
24 inherit pname version;
25 sha256 = "1hj8c98s538i0hg5mrz4bw4v07qmcl51rhxq611rj2nglnc9r25y";
26 };
27
28 propagatedBuildInputs = [
29 biopython
30 numpy
31 scipy
32 pandas
33 matplotlib
34 reportlab
35 pyfaidx
36 pysam
37 future
38 pillow
39 pomegranate
40 ];
41
42 postPatch = ''
43 substituteInPlace setup.py \
44 --replace "pandas >= 0.20.1, < 0.25.0" "pandas"
45 '';
46
47 meta = with lib; {
48 homepage = "https://cnvkit.readthedocs.io";
49 description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
50 license = licenses.asl20;
51 maintainers = [ maintainers.jbedo ];
52 };
53}