tjh.dev
1{ lib
2, buildPythonPackage
3, fetchFromGitHub
4, bzip2
5, bcftools
6, curl
7, cython
8, htslib
9, libdeflate
10, xz
11, pytestCheckHook
12, samtools
13, zlib
14}:
15
16buildPythonPackage rec {
17 pname = "pysam";
18 version = "0.21.0";
19
20 # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
21 # missing some files which cause test failures.
22 # Tracked at: https://github.com/pysam-developers/pysam/issues/616
23 src = fetchFromGitHub {
24 owner = "pysam-developers";
25 repo = "pysam";
26 rev = "refs/tags/v${version}";
27 hash = "sha256-C4/AJwcUyLoUEUEnsATLHJb5F8mltP8X2XfktYu0OTo=";
28 };
29
30 nativeBuildInputs = [ samtools ];
31
32 buildInputs = [
33 bzip2
34 curl
35 libdeflate
36 xz
37 zlib
38 ];
39
40 propagatedBuildInputs = [ cython ];
41
42 # Use nixpkgs' htslib instead of the bundled one
43 # See https://pysam.readthedocs.io/en/latest/installation.html#external
44 # NOTE that htslib should be version compatible with pysam
45 preBuild = ''
46 export HTSLIB_MODE=shared
47 export HTSLIB_LIBRARY_DIR=${htslib}/lib
48 export HTSLIB_INCLUDE_DIR=${htslib}/include
49 '';
50
51 nativeCheckInputs = [
52 pytestCheckHook
53 bcftools
54 htslib
55 ];
56
57 preCheck = ''
58 export HOME=$TMPDIR
59 make -C tests/pysam_data
60 make -C tests/cbcf_data
61 make -C tests/tabix_data
62 rm -rf pysam
63 '';
64
65 pythonImportsCheck = [
66 "pysam"
67 "pysam.bcftools"
68 "pysam.libchtslib"
69 "pysam.libcutils"
70 "pysam.libcvcf"
71 ];
72
73 meta = with lib; {
74 description = "A python module for reading, manipulating and writing genome data sets";
75 homepage = "https://pysam.readthedocs.io/";
76 maintainers = with maintainers; [ unode ];
77 license = licenses.mit;
78 platforms = platforms.unix;
79 };
80}