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{ lib
, buildPythonPackage
, fetchFromGitHub
, bzip2
, bcftools
, curl
, cython
, htslib
, 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${version}";
sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f";
};
nativeBuildInputs = [ samtools ];
buildInputs = [ bzip2 curl cython lzma zlib ];
checkInputs = [ pytest bcftools htslib ];
checkPhase = "py.test";
# tests require samtools<=1.9
doCheck = false;
preCheck = ''
export HOME=$(mktemp -d)
make -C tests/pysam_data
make -C tests/cbcf_data
'';
pythonImportsCheck = [
"pysam"
"pysam.bcftools"
"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" ];
};
}
|
