blob: 04512e8e372e8a284128039ee2dbacfebba6c70d (
plain)
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
|
{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
, samtools, hexdump, python2Packages, which }:
let
python =
python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
in stdenv.mkDerivation rec {
pname = "lumpy";
version = "0.3.0";
src = fetchFromGitHub {
owner = "arq5x";
repo = "lumpy-sv";
rev = version;
sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
};
nativeBuildInputs = [ which ];
buildInputs =
[ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
preConfigure = ''
patchShebangs ./.
# Use Nix htslib over bundled version
sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
'';
# Upstream's makefile doesn't have an install target
installPhase = ''
mkdir -p $out
cp -r bin $out
cp -r scripts $out
sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
'';
meta = with stdenv.lib; {
description = "Probabilistic structural variant caller";
homepage = "https://github.com/arq5x/lumpy-sv";
maintainers = with maintainers; [ jbedo ];
license = licenses.mit;
platforms = [ "x86_64-linux" ];
};
}
|