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{ lib
, buildPythonPackage
, fetchFromGitHub
, bzip2
, bcftools
, curl
, cython
, htslib
, libdeflate
, lzma
, 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${version}";
sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f";
};
nativeBuildInputs = [ samtools ];
buildInputs = [
bzip2
curl
cython
libdeflate
lzma
zlib
];
# Use nixpkgs' htslib instead of the bundled one
# See https://pysam.readthedocs.io/en/latest/installation.html#external
# NOTE that htslib should be version compatible with pysam
preBuild = ''
export HTSLIB_MODE=shared
export HTSLIB_LIBRARY_DIR=${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" ];
};
}
|
