forked from mirrors/nixpkgs
48 lines
1.2 KiB
Nix
48 lines
1.2 KiB
Nix
|
{ 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" ];
|
||
|
|
};
|
||
|
|
|
||
|
|
}
|