Merge remote-tracking branch 'origin/master' into staging-next

Conflicts:
 pkgs/tools/networking/xh/default.nix

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

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, python3, which, ldc, zlib }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, python3, which, ldc, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "sambamba";
@@ -12,6 +12,14 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
+  patches = [
+    # Fixes hardcoded gcc, making clang build possible.
+    (fetchpatch {
+      url = "https://github.com/biod/sambamba/commit/c50a1c91e1ba062635467f197139bf6784e9be15.patch";
+      sha256 = "1y0vlybmb9wpg4z1nca7m96mk9hxmvd3yrg7w8rxscj45hcqvf8q";
+    })
+  ];
+
   nativeBuildInputs = [ which python3 ldc ];
   buildInputs = [ zlib ];
 

pkgs/applications/science/misc/snakemake/default.nix

@@ -18,7 +18,7 @@ python3Packages.buildPythonApplication rec {
     pyyaml
     ratelimiter
     requests
-    smart_open
+    smart-open
     toposort
     wrapt
   ];