{ lib , buildPythonPackage , fetchFromGitHub , bzip2 , bcftools , curl , cython , htslib , libdeflate , xz , pytest , samtools , zlib }: buildPythonPackage rec { pname = "pysam"; version = "0.16.0.1"; # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is # missing some files which cause test failures. # Tracked at: https://github.com/pysam-developers/pysam/issues/616 src = fetchFromGitHub { owner = "pysam-developers"; repo = "pysam"; rev = "v${version}"; sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f"; }; nativeBuildInputs = [ samtools ]; buildInputs = [ bzip2 curl cython libdeflate xz zlib ]; # Use nixpkgs' htslib instead of the bundled one # See https://pysam.readthedocs.io/en/latest/installation.html#external # NOTE that htslib should be version compatible with pysam preBuild = '' export HTSLIB_MODE=shared export HTSLIB_LIBRARY_DIR=${htslib}/lib export HTSLIB_INCLUDE_DIR=${htslib}/include ''; checkInputs = [ pytest bcftools htslib ]; # See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using # disabledTests and pytestFlagsArray through pytestCheckHook checkPhase = '' # Needed to avoid /homeless-shelter error export HOME=$(mktemp -d) # To avoid API incompatibilities, these should ideally show the same version echo "> samtools --version" samtools --version echo "> htsfile --version" htsfile --version echo "> bcftools --version" bcftools --version # Create auxiliary test data make -C tests/pysam_data make -C tests/cbcf_data # Delete pysam folder in current directory to avoid importing it during testing rm -rf pysam # Deselect tests that are known to fail due to upstream issues # See https://github.com/pysam-developers/pysam/issues/961 py.test \ --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \ --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \ --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \ --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \ --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \ --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \ --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \ --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \ --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \ --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \ --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \ --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \ --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \ --deselect tests/compile_test.py::BAMTest::testCount \ tests/ ''; pythonImportsCheck = [ "pysam" "pysam.bcftools" "pysam.libchtslib" "pysam.libcutils" "pysam.libcvcf" ]; meta = with lib; { description = "A python module for reading, manipulating and writing genome data sets"; homepage = "https://pysam.readthedocs.io/"; maintainers = with maintainers; [ unode ]; license = licenses.mit; platforms = [ "i686-linux" "x86_64-linux" ]; }; }