02dab4ab5c
Long term we should move everything over to `pyproject = true`, but in the mean time we can work towards deprecating the implicit `format` paremeter. cc https://github.com/NixOS/nixpkgs/issues/253154 cc @mweinelt @figsoda
81 lines
1.7 KiB
Nix
81 lines
1.7 KiB
Nix
{ lib
|
|
, buildPythonPackage
|
|
, fetchFromGitHub
|
|
, bzip2
|
|
, bcftools
|
|
, curl
|
|
, cython
|
|
, htslib
|
|
, libdeflate
|
|
, xz
|
|
, pytestCheckHook
|
|
, samtools
|
|
, zlib
|
|
}:
|
|
|
|
buildPythonPackage rec {
|
|
pname = "pysam";
|
|
version = "0.21.0";
|
|
format = "setuptools";
|
|
|
|
# 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 = "refs/tags/v${version}";
|
|
hash = "sha256-C4/AJwcUyLoUEUEnsATLHJb5F8mltP8X2XfktYu0OTo=";
|
|
};
|
|
|
|
nativeBuildInputs = [ samtools ];
|
|
|
|
buildInputs = [
|
|
bzip2
|
|
curl
|
|
libdeflate
|
|
xz
|
|
zlib
|
|
];
|
|
|
|
propagatedBuildInputs = [ cython ];
|
|
|
|
# Use nixpkgs' htslib instead of the bundled one
|
|
# See https://pysam.readthedocs.io/en/latest/installation.html#external
|
|
# NOTE that htslib should be version compatible with pysam
|
|
preBuild = ''
|
|
export HTSLIB_MODE=shared
|
|
export HTSLIB_LIBRARY_DIR=${htslib}/lib
|
|
export HTSLIB_INCLUDE_DIR=${htslib}/include
|
|
'';
|
|
|
|
nativeCheckInputs = [
|
|
pytestCheckHook
|
|
bcftools
|
|
htslib
|
|
];
|
|
|
|
preCheck = ''
|
|
export HOME=$TMPDIR
|
|
make -C tests/pysam_data
|
|
make -C tests/cbcf_data
|
|
make -C tests/tabix_data
|
|
rm -rf pysam
|
|
'';
|
|
|
|
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 = platforms.unix;
|
|
};
|
|
}
|