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{ lib
, buildPythonPackage
, fetchFromGitHub
, bzip2
, bcftools
, curl
, cython
, htslib
, lzma
, pytest
, samtools
, zlib
}:
buildPythonPackage rec {
pname = "pysam";
version = "0.15.3";
# 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${version}";
sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb";
};
buildInputs = [ bzip2 curl cython lzma zlib ];
checkInputs = [ pytest bcftools htslib samtools ];
checkPhase = "py.test";
preInstall = ''
export HOME=$(mktemp -d)
make -C tests/pysam_data
make -C tests/cbcf_data
'';
meta = {
homepage = http://pysam.readthedocs.io/;
description = "A python module for reading, manipulating and writing genome data sets";
maintainers = with lib.maintainers; [ unode ];
license = lib.licenses.mit;
platforms = [ "i686-linux" "x86_64-linux" ];
};
}
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