114 lines
3.7 KiB
Nix
114 lines
3.7 KiB
Nix
{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, bzip2
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, bcftools
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, curl
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, cython
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, htslib
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, libdeflate
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, xz
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, pytest
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, samtools
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, zlib
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}:
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buildPythonPackage rec {
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pname = "pysam";
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version = "0.19.1";
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# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
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# missing some files which cause test failures.
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# Tracked at: https://github.com/pysam-developers/pysam/issues/616
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src = fetchFromGitHub {
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owner = "pysam-developers";
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repo = "pysam";
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rev = "refs/tags/v${version}";
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sha256 = "sha256-fbvfobffLha1eFatnHvh0tOYcuMRLTmy/BJ9QXFHx2o=";
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};
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nativeBuildInputs = [ samtools ];
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buildInputs = [
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bzip2
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curl
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cython
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libdeflate
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xz
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zlib
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];
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# Use nixpkgs' htslib instead of the bundled one
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# See https://pysam.readthedocs.io/en/latest/installation.html#external
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# NOTE that htslib should be version compatible with pysam
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preBuild = ''
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export HTSLIB_MODE=shared
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export HTSLIB_LIBRARY_DIR=${htslib}/lib
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export HTSLIB_INCLUDE_DIR=${htslib}/include
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'';
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checkInputs = [
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pytest
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bcftools
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htslib
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];
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# See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using
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# disabledTests and pytestFlagsArray through pytestCheckHook
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checkPhase = ''
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# Needed to avoid /homeless-shelter error
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export HOME=$(mktemp -d)
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# To avoid API incompatibilities, these should ideally show the same version
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echo "> samtools --version"
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samtools --version
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echo "> htsfile --version"
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htsfile --version
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echo "> bcftools --version"
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bcftools --version
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# Create auxiliary test data
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make -C tests/pysam_data
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make -C tests/cbcf_data
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# Delete pysam folder in current directory to avoid importing it during testing
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rm -rf pysam
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# Deselect tests that are known to fail due to upstream issues
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# See https://github.com/pysam-developers/pysam/issues/961
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py.test \
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--deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \
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--deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
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--deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
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--deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
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--deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
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--deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
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--deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
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--deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
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--deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
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--deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
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--deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
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--deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
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--deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
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--deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
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--deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
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--deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
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--deselect tests/compile_test.py::BAMTest::testCount \
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tests/
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'';
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pythonImportsCheck = [
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"pysam"
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"pysam.bcftools"
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"pysam.libchtslib"
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"pysam.libcutils"
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"pysam.libcvcf"
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];
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meta = with lib; {
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description = "A python module for reading, manipulating and writing genome data sets";
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homepage = "https://pysam.readthedocs.io/";
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maintainers = with maintainers; [ unode ];
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license = licenses.mit;
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platforms = platforms.unix;
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};
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}
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