depot/third_party/nixpkgs/pkgs/applications/science/biology/bedops/default.nix

63 lines
1.9 KiB
Nix

{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
stdenv.mkDerivation rec {
pname = "bedops";
version = "2.4.41";
src = fetchFromGitHub {
owner = "bedops";
repo = "bedops";
rev = "v${version}";
sha256 = "sha256-VJBoi1+tHA4oOVOsClUfimB+mOV5ZSQsDcDq3vAZwBA=";
};
buildInputs = [ zlib bzip2 jansson ];
nativeBuildInputs = [ makeWrapper ];
preConfigure = ''
# We use nixpkgs versions of these libraries
rm -r third-party
sed -i '/^LIBS/d' system.mk/*
sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile*
# `make support` installs above libraries
substituteInPlace system.mk/* \
--replace ": support" ":"
# Variable name is different in this makefile
substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
--replace "DIST_DIR" "BINDIR"
# `mkdir -p $BINDIR` is missing
substituteInPlace applications/bed/sort-bed/src/Makefile.darwin \
--replace 'mkdir -p ''${OBJ_DIR}' 'mkdir -p ''${OBJ_DIR} ''${BINDIR}'
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;
};
}