mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-12-22 13:43:22 +00:00
459c5ec3b1
These will be fixed upstream and are due to format changes introduced in samtools and htslib 1.11
115 lines
3.7 KiB
Nix
115 lines
3.7 KiB
Nix
{ 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" ];
|
|
};
|
|
}
|