1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
{ 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;
};
}
|