Merge staging-next into staging

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/development/libraries/libfyaml/default.nix

@@ -2,21 +2,17 @@
 
 stdenv.mkDerivation rec {
   pname = "libfyaml";
-  version = "0.6";
+  version = "0.6.3";
 
   src = fetchFromGitHub {
     owner = "pantoniou";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0b1wnalh49rbjykw4bj5k3y1d9yr8k6f0im221bl1gyrwlgw7hp5";
+    sha256 = "1aw5s0ns79jr3lpcy3hdsrlr79rrv5aqymv4h43axvy2bi90nrr0";
   };
 
   nativeBuildInputs = [ autoreconfHook pkg-config ];
 
-  postPatch = ''
-    echo ${version} > .tarball-version
-  '';
-
   meta = with lib; {
     homepage = "https://github.com/pantoniou/libfyaml";
     description = "Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the full YAML testsuite";

pkgs/development/python-modules/lightgbm/default.nix

@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "lightgbm";
-  version = "3.1.1";
+  version = "3.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "babece2e3613e97748a67ed45387bb0e984bdb1f4126e39f010fbfe7503c7b20";
+    sha256 = "000c6e0e225834a8a94a84571cf41e4b7c7b97a0db6d286c1237de8ba6066726";
   };
 
   nativeBuildInputs = [

pkgs/os-specific/linux/compsize/default.nix

@@ -13,11 +13,12 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ btrfs-progs ];
 
-  installPhase = ''
-    mkdir -p $out/bin
+  installFlags = [
+    "PREFIX=${placeholder "out"}"
+  ];
+
+  preInstall = ''
     mkdir -p $out/share/man/man8
-    install -m 0755 compsize $out/bin
-    install -m 0444 compsize.8 $out/share/man/man8
   '';
 
   meta = with lib; {

pkgs/servers/sql/postgresql/ext/pg_auto_failover.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pg_auto_failover";
-  version = "1.4.2";
+  version = "1.5.1";
 
   src = fetchFromGitHub {
     owner = "citusdata";
     repo = pname;
     rev = "v${version}";
-    sha256 = "030vm83ksfi4daypr4hamvvfs4g1ckww4ldg7rrk6c6hqkppykpa";
+    sha256 = "14bh3cqkdd1z16iy0lmv8a3f8gmmink1nzhf5jhkd0n6g7r65p6d";
   };
 
   buildInputs = [ postgresql openssl zlib readline ];
@@ -23,6 +23,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     description = "PostgreSQL extension and service for automated failover and high-availability";
     homepage = "https://github.com/citusdata/pg_auto_failover";
+    changelog = "https://github.com/citusdata/pg_auto_failover/raw/v${version}/CHANGELOG.md";
     maintainers = [ maintainers.marsam ];
     platforms = postgresql.meta.platforms;
     license = licenses.postgresql;

pkgs/top-level/all-packages.nix

@@ -28142,6 +28142,8 @@ 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 { };