blob: b5743df9a7ca474ff0124cf708a18ef25bb3a409 (
plain) (
blame)
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
|
{ lib, stdenv, fetchurl, fetchpatch, zlib, htslib, perl, ncurses ? null }:
stdenv.mkDerivation rec {
pname = "samtools";
version = "1.18";
src = fetchurl {
url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
sha256 = "sha256-1ob/piECO6YYIqKlC3DoXQsY55Nx3lrbB4KFGdP8BuE=";
};
# tests require `bgzip` from the htslib package
nativeCheckInputs = [ htslib ];
nativeBuildInputs = [ perl ];
buildInputs = [ zlib ncurses htslib ];
preConfigure = lib.optional stdenv.hostPlatform.isStatic ''
export LIBS="-lz -lbz2 -llzma"
'';
makeFlags = lib.optional stdenv.hostPlatform.isStatic "AR=${stdenv.cc.targetPrefix}ar";
configureFlags = [ "--with-htslib=${htslib}" ]
++ lib.optional (ncurses == null) "--without-curses"
++ lib.optionals stdenv.hostPlatform.isStatic ["--without-curses" ]
;
preCheck = ''
patchShebangs test/
'';
enableParallelBuilding = true;
doCheck = true;
meta = with lib; {
description = "Tools for manipulating SAM/BAM/CRAM format";
license = licenses.mit;
homepage = "http://www.htslib.org/";
platforms = platforms.unix;
maintainers = with maintainers; [ mimame unode ];
};
}
|