pyrox.dev
1{ lib
2, buildPythonPackage
3, fetchFromGitHub
4, bzip2
5, bcftools
6, curl
7, cython
8, htslib
9, libdeflate
10, xz
11, pytest
12, samtools
13, zlib
14}:
15
16buildPythonPackage rec {
17 pname = "pysam";
18 version = "0.17.0";
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 = "v${version}";
27 sha256 = "sha256-RDeBq6pwBGCBNIn8YOPQr96GuL6FKEYeLAPQD6XN0iE=";
28 };
29
30 nativeBuildInputs = [ samtools ];
31 buildInputs = [
32 bzip2
33 curl
34 cython
35 libdeflate
36 xz
37 zlib
38 ];
39
40 # Use nixpkgs' htslib instead of the bundled one
41 # See https://pysam.readthedocs.io/en/latest/installation.html#external
42 # NOTE that htslib should be version compatible with pysam
43 preBuild = ''
44 export HTSLIB_MODE=shared
45 export HTSLIB_LIBRARY_DIR=${htslib}/lib
46 export HTSLIB_INCLUDE_DIR=${htslib}/include
47 '';
48
49 checkInputs = [
50 pytest
51 bcftools
52 htslib
53 ];
54
55 # See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using
56 # disabledTests and pytestFlagsArray through pytestCheckHook
57 checkPhase = ''
58 # Needed to avoid /homeless-shelter error
59 export HOME=$(mktemp -d)
60
61 # To avoid API incompatibilities, these should ideally show the same version
62 echo "> samtools --version"
63 samtools --version
64 echo "> htsfile --version"
65 htsfile --version
66 echo "> bcftools --version"
67 bcftools --version
68
69 # Create auxiliary test data
70 make -C tests/pysam_data
71 make -C tests/cbcf_data
72
73 # Delete pysam folder in current directory to avoid importing it during testing
74 rm -rf pysam
75
76 # Deselect tests that are known to fail due to upstream issues
77 # See https://github.com/pysam-developers/pysam/issues/961
78 py.test \
79 --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \
80 --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
81 --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
82 --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
83 --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
84 --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
85 --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
86 --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
87 --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
88 --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
89 --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
90 --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
91 --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
92 --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
93 --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
94 --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
95 --deselect tests/compile_test.py::BAMTest::testCount \
96 tests/
97 '';
98
99 pythonImportsCheck = [
100 "pysam"
101 "pysam.bcftools"
102 "pysam.libchtslib"
103 "pysam.libcutils"
104 "pysam.libcvcf"
105 ];
106
107 meta = with lib; {
108 description = "A python module for reading, manipulating and writing genome data sets";
109 homepage = "https://pysam.readthedocs.io/";
110 maintainers = with maintainers; [ unode ];
111 license = licenses.mit;
112 platforms = [ "i686-linux" "x86_64-linux" ];
113 };
114}