2018-02-02 01:24:06 +00:00
|
|
|
{ lib
|
|
|
|
|
, buildPythonPackage
|
|
|
|
|
, fetchFromGitHub
|
|
|
|
|
, bzip2
|
|
|
|
|
, bcftools
|
|
|
|
|
, curl
|
|
|
|
|
, cython
|
|
|
|
|
, htslib
|
|
|
|
|
, lzma
|
|
|
|
|
, pytest
|
|
|
|
|
, samtools
|
|
|
|
|
, zlib
|
|
|
|
|
}:
|
|
|
|
|
|
|
|
|
|
buildPythonPackage rec {
|
|
|
|
|
pname = "pysam";
|
2019-10-05 09:00:55 +00:00
|
|
|
version = "0.15.3";
|
2018-02-02 01:24:06 +00:00
|
|
|
|
|
|
|
|
# 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${version}";
|
2019-10-05 09:00:55 +00:00
|
|
|
sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb";
|
2018-02-02 01:24:06 +00:00
|
|
|
};
|
|
|
|
|
|
|
|
|
|
buildInputs = [ bzip2 curl cython lzma zlib ];
|
|
|
|
|
|
|
|
|
|
checkInputs = [ pytest bcftools htslib samtools ];
|
|
|
|
|
|
|
|
|
|
checkPhase = "py.test";
|
|
|
|
|
|
|
|
|
|
preInstall = ''
|
|
|
|
|
export HOME=$(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" ];
|
|
|
|
|
};
|
|
|
|
|
}
|
