pkgs/development/python-modules/pysam/default.nix

   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
  16 buildPythonPackage rec {
  17   pname   = "pysam";
  18   version = "0.16.0.1";
  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${version}";
  27     sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f";
  28   };
  29
  30   nativeBuildInputs = [ samtools ];
  31   buildInputs = [
  32     bzip2
  33     curl
  34     cython
  35     libdeflate
  36     xz
  37     zlib
  38   ];
  39
  40   # Use nixpkgs' htslib instead of the bundled one
  41   # See https://pysam.readthedocs.io/en/latest/installation.html#external
  42   # NOTE that htslib should be version compatible with pysam
  43   preBuild = ''
  44     export HTSLIB_MODE=shared
  45     export HTSLIB_LIBRARY_DIR=${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 }