bedops: init 2.4.39

pkgs/applications/science/biology/bedops/default.nix

@@ -0,0 +1,51 @@
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  pname = "bedops";
+  version = "2.4.39";
+
+  src = fetchFromGitHub {
+    owner = "bedops";
+    repo = "bedops";
+    rev = "v${version}";
+    sha256 = "sha256-vPrut3uhZK1Eg9vPcyxVNWW4zKeypdsb28oM1xbbpJo=";
+  };
+
+  buildInputs = [ zlib bzip2 jansson ];
+  nativeBuildInputs = [ makeWrapper ];
+
+  preConfigure = ''
+    # We use nixpkgs versions of these libraries
+    rm -r third-party
+    sed -i '/^LIBS/d' system.mk/*
+    sed -i 's|^LIBRARIES.*$|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;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -28140,6 +28140,8 @@ in
 
   bayescan = callPackage ../applications/science/biology/bayescan { };
 
+  bedops = callPackage ../applications/science/biology/bedops { };
+
   bedtools = callPackage ../applications/science/biology/bedtools { };
 
   bcftools = callPackage ../applications/science/biology/bcftools { };