tjh.dev
1{
2 lib,
3 python3Packages,
4 fetchFromGitHub,
5 addBinToPathHook,
6}:
7
8python3Packages.buildPythonApplication rec {
9 pname = "deeptools";
10 version = "3.5.6";
11 pyproject = true;
12
13 src = fetchFromGitHub {
14 owner = "deeptools";
15 repo = "deepTools";
16 tag = version;
17 hash = "sha256-dxXlOvOjF4KSc5YO+1A5hlp95sfeyPSbmp93tihm7Vo=";
18 };
19
20 build-system = with python3Packages; [
21 setuptools
22 ];
23
24 dependencies = with python3Packages; [
25 numpy
26 scipy
27 matplotlib
28 pysam
29 numpydoc
30 pybigwig
31 py2bit
32 plotly
33 deeptoolsintervals
34 ];
35
36 nativeCheckInputs = with python3Packages; [
37 pytestCheckHook
38 addBinToPathHook
39 ];
40
41 disabledTestPaths = [
42 # tests trip on `len(sys.argv) == 1`
43 "deeptools/test/test_bigwigAverage.py"
44 "deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py"
45 "deeptools/test/test_heatmapper.py"
46 "deeptools/test/test_multiBamSummary.py"
47 ];
48
49 meta = {
50 homepage = "https://deeptools.readthedocs.io/en/develop";
51 description = "Tools for exploring deep DNA sequencing data";
52 longDescription = ''
53 deepTools contains useful modules to process the mapped reads data for multiple
54 quality checks, creating normalized coverage files in standard bedGraph and bigWig
55 file formats, that allow comparison between different files (for example, treatment and control).
56 Finally, using such normalized and standardized files, deepTools can create many
57 publication-ready visualizations to identify enrichments and for functional
58 annotations of the genome.
59 '';
60 license = with lib.licenses; [
61 mit
62 bsd3
63 ];
64 maintainers = with lib.maintainers; [ scalavision ];
65 };
66}