nixpkgs/pkgs/applications/science/biology/bedops/default.nix
2021-07-23 01:02:40 +00:00

52 lines
1.5 KiB
Nix

{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
stdenv.mkDerivation rec {
pname = "bedops";
version = "2.4.40";
src = fetchFromGitHub {
owner = "bedops";
repo = "bedops";
rev = "v${version}";
sha256 = "sha256-rJVl3KbzGblyQZ7FtJXeEv/wjQJmzYGNjzhvkoMoBWY=";
};
buildInputs = [ zlib bzip2 jansson ];
nativeBuildInputs = [ makeWrapper ];
preConfigure = ''
# We use nixpkgs versions of these libraries
rm -r third-party
sed -i '/^LIBS/d' system.mk/*
sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile
substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' ""
# Function name is different in nixpkgs provided libraries
for f in interfaces/src/data/starch/starchFileHelpers.c applications/bed/starch/src/starchcat.c ; do
substituteInPlace $f --replace deflateInit2cpp deflateInit2
done
# Don't force static
for f in */*/*/*/Makefile ; do
substituteInPlace $f --replace '-static' ""
done
'';
makeFlags = [ "BINDIR=$(out)/bin" ];
postFixup = ''
for f in $out/bin/* ; do
wrapProgram $f --prefix PATH : "$out/bin"
done
'';
meta = with lib; {
description = "Suite of tools for addressing questions arising in genomics studies";
homepage = "https://github.com/bedops/bedops";
license = licenses.gpl2Only;
maintainers = with maintainers; [ jbedo ];
platforms = platforms.x86_64;
broken = stdenv.isDarwin;
};
}