tjh.dev
1{ lib
2, buildPythonPackage
3, fetchFromGitHub
4, bzip2
5, bcftools
6, curl
7, cython
8, htslib
9, lzma
10, pytest
11, samtools
12, zlib
13}:
14
15buildPythonPackage rec {
16 pname = "pysam";
17 version = "0.15.2";
18
19 # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
20 # missing some files which cause test failures.
21 # Tracked at: https://github.com/pysam-developers/pysam/issues/616
22 src = fetchFromGitHub {
23 owner = "pysam-developers";
24 repo = "pysam";
25 rev = "v${version}";
26 sha256 = "03aczbzx6gmvgy60fhswpwkry7a8zb5q1pbp55v5gx8hk15n40k1";
27 };
28
29 buildInputs = [ bzip2 curl cython lzma zlib ];
30
31 checkInputs = [ pytest bcftools htslib samtools ];
32
33 checkPhase = "py.test";
34
35 preInstall = ''
36 export HOME=$(mktemp -d)
37 make -C tests/pysam_data
38 make -C tests/cbcf_data
39 '';
40
41 meta = {
42 homepage = http://pysam.readthedocs.io/;
43 description = "A python module for reading, manipulating and writing genome data sets";
44 maintainers = with lib.maintainers; [ unode ];
45 license = lib.licenses.mit;
46 platforms = [ "i686-linux" "x86_64-linux" ];
47 };
48}