From aafffb261429688e93a88269bdb03c0cbf884085 Mon Sep 17 00:00:00 2001
From: Bruno Bzeznik <Bruno.Bzeznik@imag.fr>
Date: Fri, 14 Jun 2019 16:31:39 +0200
Subject: [PATCH 01/27] trimal: init at 1.4.1

---
 .../science/biology/trimal/default.nix        | 31 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 33 insertions(+)
 create mode 100755 pkgs/applications/science/biology/trimal/default.nix

diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix
new file mode 100755
index 00000000000..d4e8fee7bc3
--- /dev/null
+++ b/pkgs/applications/science/biology/trimal/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "trimal";
+  version = "1.4.1";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "scapella";
+    rev = "v${version}";
+    sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0";
+  };
+
+  postUnpack = ''
+    sourceRoot=''${sourceRoot}/source
+    echo Source root reset to ''${sourceRoot}
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -a trimal readal statal $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment";
+    license = licenses.gpl3;
+    platforms = platforms.linux;
+    homepage = http://trimal.cgenomics.org;
+    maintainers = [ maintainers.bzizou ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1a9a1c54b3a..f3bcadfe1e5 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21971,6 +21971,8 @@ in
 
   seaview = callPackage ../applications/science/biology/seaview { };
 
+  trimal = callPackage ../applications/science/biology/trimal { };
+
   varscan = callPackage ../applications/science/biology/varscan { };
 
   hmmer = callPackage ../applications/science/biology/hmmer { };

From 19d91206e7fb22b93d866f6b7d3c99120299a3df Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Tue, 6 Aug 2019 15:42:10 -0700
Subject: [PATCH 02/27] vulkan-*: 1.1.106 -> 1.1.114.0

---
 .../libraries/vulkan-headers/default.nix      |  4 +-
 .../libraries/vulkan-loader/default.nix       |  8 ++--
 .../vulkan-loader/system-search-path.patch    | 45 -------------------
 .../vulkan-validation-layers/default.nix      |  9 ++--
 pkgs/tools/graphics/vulkan-tools/default.nix  |  4 +-
 pkgs/top-level/all-packages.nix               | 12 ++---
 6 files changed, 18 insertions(+), 64 deletions(-)
 delete mode 100644 pkgs/development/libraries/vulkan-loader/system-search-path.patch

diff --git a/pkgs/development/libraries/vulkan-headers/default.nix b/pkgs/development/libraries/vulkan-headers/default.nix
index f7c1bf9a65b..9e3886c264e 100644
--- a/pkgs/development/libraries/vulkan-headers/default.nix
+++ b/pkgs/development/libraries/vulkan-headers/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, cmake }:
 stdenv.mkDerivation rec {
   name = "vulkan-headers-${version}";
-  version = "1.1.106";
+  version = "1.1.114.0";
 
   buildInputs = [ cmake ];
 
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     owner = "KhronosGroup";
     repo = "Vulkan-Headers";
     rev = "sdk-${version}";
-    sha256 = "0idw7q715ikj575qmspvgq2gzc6c1sj581b8z3xnv6wz9qbzrmsd";
+    sha256 = "0fdvh26nxibylh32lj8b62d9nf9j25xa0il9zg362wmr2zgm8gka";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/vulkan-loader/default.nix b/pkgs/development/libraries/vulkan-loader/default.nix
index a44e91e1bf5..dd09d5d3c7c 100644
--- a/pkgs/development/libraries/vulkan-loader/default.nix
+++ b/pkgs/development/libraries/vulkan-loader/default.nix
@@ -2,7 +2,7 @@
 , xlibsWrapper, libxcb, libXrandr, libXext, wayland, addOpenGLRunpath }:
 
 let
-  version = "1.1.106";
+  version = "1.1.114.0";
 in
 
 assert version == vulkan-headers.version;
@@ -14,17 +14,15 @@ stdenv.mkDerivation rec {
     owner = "KhronosGroup";
     repo = "Vulkan-Loader";
     rev = "sdk-${version}";
-    sha256 = "0zhrwj1gi90x2w8gaaaw5h4b969a8gfy244kn0drrplhhb1nqz3b";
+    sha256 = "08nibkbjf3g32qyp5bpdvj7i0zdv5ds1n5y52z8pvyzkpiz7s6ww";
   };
 
   nativeBuildInputs = [ pkgconfig addOpenGLRunpath ];
   buildInputs = [ cmake python3 xlibsWrapper libxcb libXrandr libXext wayland ];
   enableParallelBuilding = true;
 
-  patches = [ ./system-search-path.patch ];
-
   cmakeFlags = [
-    "-DSYSTEM_SEARCH_PATH=${addOpenGLRunpath.driverLink}/share"
+    "-DSYSCONFDIR=${addOpenGLRunpath.driverLink}/share"
     "-DVULKAN_HEADERS_INSTALL_DIR=${vulkan-headers}"
   ];
 
diff --git a/pkgs/development/libraries/vulkan-loader/system-search-path.patch b/pkgs/development/libraries/vulkan-loader/system-search-path.patch
deleted file mode 100644
index 26f83e6d534..00000000000
--- a/pkgs/development/libraries/vulkan-loader/system-search-path.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 9ac5ce835..cbdb0ff56 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -88,6 +88,12 @@ if(UNIX)
-             STRING
-             "Search path to use when XDG_DATA_DIRS is unset or empty or the current process is SUID/SGID. Default is freedesktop compliant."
-         )
-+    set(
-+        SYSTEM_SEARCH_PATH ""
-+        CACHE
-+            STRING
-+            "Search path to always use, after all other search paths."
-+    )
- endif()
- 
- if(UNIX AND NOT APPLE) # i.e.: Linux
-@@ -184,6 +190,7 @@ if(UNIX)
-     add_definitions(-DFALLBACK_CONFIG_DIRS="${FALLBACK_CONFIG_DIRS}")
-     add_definitions(-DFALLBACK_DATA_DIRS="${FALLBACK_DATA_DIRS}")
-     add_definitions(-DSYSCONFDIR="${CMAKE_INSTALL_FULL_SYSCONFDIR}")
-+    add_definitions(-DSYSTEM_SEARCH_PATH="${SYSTEM_SEARCH_PATH}")
- 
-     # Make sure /etc is searched by the loader
-     if(NOT (CMAKE_INSTALL_FULL_SYSCONFDIR STREQUAL "/etc"))
-diff --git a/loader/loader.c b/loader/loader.c
-index 0d3b5a947..abe357004 100644
---- a/loader/loader.c
-+++ b/loader/loader.c
-@@ -3688,6 +3688,7 @@ static VkResult ReadDataFilesInSearchPaths(const struct loader_instance *inst, e
-                 search_path_size += DetermineDataFilePathSize(xdgdatahome, rel_size);
-                 search_path_size += DetermineDataFilePathSize(home_root, rel_size);
-             }
-+            search_path_size += DetermineDataFilePathSize(SYSTEM_SEARCH_PATH, rel_size);
- #endif
-         }
-     }
-@@ -3737,6 +3738,7 @@ static VkResult ReadDataFilesInSearchPaths(const struct loader_instance *inst, e
-                 CopyDataFilePath(xdgdatahome, relative_location, rel_size, &cur_path_ptr);
-                 CopyDataFilePath(home_root, relative_location, rel_size, &cur_path_ptr);
-             }
-+            CopyDataFilePath(SYSTEM_SEARCH_PATH, relative_location, rel_size, &cur_path_ptr);
-         }
- 
-         // Remove the last path separator
diff --git a/pkgs/development/tools/vulkan-validation-layers/default.nix b/pkgs/development/tools/vulkan-validation-layers/default.nix
index 3c189d09f1c..36d018682df 100644
--- a/pkgs/development/tools/vulkan-validation-layers/default.nix
+++ b/pkgs/development/tools/vulkan-validation-layers/default.nix
@@ -1,15 +1,16 @@
 { stdenv, fetchFromGitHub, cmake, writeText, python3
 , vulkan-headers, vulkan-loader, glslang
-, pkgconfig, xlibsWrapper, libxcb, libXrandr, wayland }:
+, pkgconfig, xlibsWrapper, libxcb, libXrandr, wayland, spirv-headers }:
+
 stdenv.mkDerivation rec {
-  name = "vulkan-validation-layers-${version}";
-  version = "1.1.106.0"; # WARNING: glslang overrides in all-packages.nix must be updated to match known-good.json!
+  pname = "vulkan-validation-layers";
+  version = "1.1.114.0";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "Vulkan-ValidationLayers";
     rev = "sdk-${version}";
-    sha256 = "1sq42j8ikll2dyi9ygaz80lx89mvq9d21pkaf49gzhg4xjcd97dp";
+    sha256 = "0f8dlrjw1nz2adhzi4sbvljys4h0dyiwafdihsdyrg3xncgffks4";
   };
 
   nativeBuildInputs = [ pkgconfig cmake python3  ];
diff --git a/pkgs/tools/graphics/vulkan-tools/default.nix b/pkgs/tools/graphics/vulkan-tools/default.nix
index 320b4eed14c..c02054cfbd6 100644
--- a/pkgs/tools/graphics/vulkan-tools/default.nix
+++ b/pkgs/tools/graphics/vulkan-tools/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "vulkan-tools-${version}";
-  version = "1.1.106.0";
+  version = "1.1.114.0";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "Vulkan-Tools";
     rev = "sdk-${version}";
-    sha256 = "0swqyk16mbkivyk79dpqbhpw05a7yrakqynywznr5zgqbc0z4gj8";
+    sha256 = "1d4fcy11gk21x7r7vywdcc1dy9j1d2j78hvd5vfh3vy9fnahx107";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f5b089be81b..073e8fcb5c6 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13828,24 +13828,24 @@ in
         src = fetchFromGitHub {
           owner = "KhronosGroup";
           repo = "SPIRV-Tools";
-          rev = "26c1b8878315a7a5c188df45e0bc236bb222b698";
-          sha256 = "1q76vaqwxf4q2l4rd7j2p2jqgcqpys0m235drzx0drkn2qd50n1b";
+          rev = "aa9e8f538041db3055ea443080e0ccc315fa114f";
+          sha256 = "1nbii0xa5zgs36dmpvzpli1jbzb9ijr7bkgvzmlpcjrjsl02cnbk";
         };
       });
       spirv-headers = spirv-tools.overrideAttrs (_: {
         src = fetchFromGitHub {
           owner = "KhronosGroup";
           repo = "SPIRV-Headers";
-          rev = "2434b89345a50c018c84f42a310b0fad4f3fd94f";
-          sha256 = "1m902q1alm0rbh69zlskkx4n453xijijp9mf3wzwphi2j36gygwm";
+          rev = "45c2cc37276d69e5b257507d97fd90d2a5684ccc";
+          sha256 = "1jrzazv5j8nsn8hz5vc43vz4msps05d65wdy9spfg2hg36r1s2pm";
         };
       });
     }).overrideAttrs (_: {
       src = fetchFromGitHub {
         owner = "KhronosGroup";
         repo = "glslang";
-        rev = "e06c7e9a515b716c731bda13f507546f107775d1";
-        sha256 = "04y4dd1cqdkd4qffmhgmg3agf9j07ii2w38vpp4jw53ir818bqdq";
+        rev = "333d1c95792692205472c457d7bec915a94c8000";
+        sha256 = "04srq1zcilhs7p1xz7wcnrncjxqskhfnqggisvxw5f774gk01ks6";
       };
     });
   };

From cf73f645501ef5be263955d940b4effb0b870d5a Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Tue, 6 Aug 2019 15:45:23 -0700
Subject: [PATCH 03/27] glslang: 7.11.3113 -> 7.11.3214

---
 .../development/compilers/glslang/default.nix | 26 ++++++++++++++-----
 pkgs/top-level/all-packages.nix               | 12 ++++-----
 2 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/compilers/glslang/default.nix b/pkgs/development/compilers/glslang/default.nix
index 3c46dfc107b..161e57b5479 100644
--- a/pkgs/development/compilers/glslang/default.nix
+++ b/pkgs/development/compilers/glslang/default.nix
@@ -1,16 +1,29 @@
-{ stdenv, fetchFromGitHub, cmake, bison, jq, python, spirv-tools, spirv-headers }:
+{ stdenv, fetchFromGitHub
+, bison
+, cmake
+, jq
+, python3
+, spirv-headers
+, spirv-tools
+}:
+
 stdenv.mkDerivation rec {
-  name = "glslang-${version}";
-  version = "7.11.3113";
+  pname = "glslang";
+  version = "7.11.3214";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "glslang";
-    rev = "${version}";
-    sha256 = "1kzv2b4q1fddxd7c0hc754nd6rw6y9vijb9fsi13xzzq9dficgb6";
+    rev = version;
+    sha256 = "0dqjga0lcza006fhac26zp2plbq4gx8a6nsmrwkqlzji6lw1jins";
   };
 
-  nativeBuildInputs = [ cmake python bison jq ];
+  # These get set at all-packages, keep onto them for child drvs
+  passthru = {
+    inherit spirv-tools spirv-headers;
+  };
+
+  nativeBuildInputs = [ cmake python3 bison jq ];
   enableParallelBuilding = true;
 
   postPatch = ''
@@ -18,6 +31,7 @@ stdenv.mkDerivation rec {
     ln -s "${spirv-headers.src}" External/spirv-tools/external/spirv-headers
   '';
 
+  # Ensure spirv-headers and spirv-tools match exactly to what is expected
   preConfigure = ''
     HEADERS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools/external/spirv-headers"))[0].commit')
     TOOLS_COMMIT=$(jq -r < known_good.json '.commits|map(select(.name=="spirv-tools"))[0].commit')
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 073e8fcb5c6..99e09962d8e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -7727,16 +7727,16 @@ in
       src = fetchFromGitHub {
         owner = "KhronosGroup";
         repo = "SPIRV-Tools";
-        rev = "117a1fd11f11e9bef9faa563c3d5156cc6ab529c";
-        sha256 = "1w5hb6sgy71g279wsghixxc75r7rsm7wki011mpz039q66827sym";
+        rev = "26c1b8878315a7a5c188df45e0bc236bb222b698";
+        sha256 = "1q76vaqwxf4q2l4rd7j2p2jqgcqpys0m235drzx0drkn2qd50n1b";
       };
     });
-    spirv-headers = spirv-tools.overrideAttrs (_: {
+    spirv-headers = spirv-headers.overrideAttrs (_: {
       src = fetchFromGitHub {
         owner = "KhronosGroup";
-        repo = "SPIRV-Tools";
-        rev = "79b6681aadcb53c27d1052e5f8a0e82a981dbf2f";
-        sha256 = "0flng2rdmc4ndq3j71h6wk1ibcjvhjrg2rzd6rv445vcsf0jh2pj";
+        repo = "SPIRV-Headers";
+        rev = "2434b89345a50c018c84f42a310b0fad4f3fd94f";
+        sha256 = "1m902q1alm0rbh69zlskkx4n453xijijp9mf3wzwphi2j36gygwm";
       };
     });
   };

From ecd78af013c039c85dffef3a5451878dc684e3ac Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Tue, 6 Aug 2019 15:48:24 -0700
Subject: [PATCH 04/27] spirv-headers: 2019.1 -> 1.4.1

---
 pkgs/development/libraries/spirv-headers/default.nix | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/libraries/spirv-headers/default.nix b/pkgs/development/libraries/spirv-headers/default.nix
index 40d272fd07d..9b2c0032d4e 100644
--- a/pkgs/development/libraries/spirv-headers/default.nix
+++ b/pkgs/development/libraries/spirv-headers/default.nix
@@ -1,13 +1,14 @@
 { stdenv, fetchFromGitHub, cmake }:
+
 stdenv.mkDerivation rec {
-  name = "spirv-headers-${version}";
-  version = "2019.1"; # spirv-tools version whose DEPS file calls for this commit
+  pname = "spirv-headers";
+  version = "1.4.1";
 
   src = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "SPIRV-Headers";
-    rev = "79b6681aadcb53c27d1052e5f8a0e82a981dbf2f"; # from spirv-tools' DEPS
-    sha256 = "0flng2rdmc4ndq3j71h6wk1ibcjvhjrg2rzd6rv445vcsf0jh2pj";
+    rev = version;
+    sha256 = "1zfmvg3x0q9w652s8g5m5rcckzm6jiiw8rif2qck4vlsryl55akp";
   };
 
   nativeBuildInputs = [ cmake ];

From 96a64ff735c61be49f42aa6ae5e44998658a7d65 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Tue, 6 Aug 2019 15:48:54 -0700
Subject: [PATCH 05/27] spirv-tools: 2019.1 -> 2019.3

---
 pkgs/development/tools/spirv-tools/default.nix | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/tools/spirv-tools/default.nix b/pkgs/development/tools/spirv-tools/default.nix
index c9df2703daa..85b82318439 100644
--- a/pkgs/development/tools/spirv-tools/default.nix
+++ b/pkgs/development/tools/spirv-tools/default.nix
@@ -1,10 +1,9 @@
-{ stdenv, fetchFromGitHub, cmake, python, spirv-headers }:
+{ stdenv, fetchFromGitHub, cmake, python3, spirv-headers }:
 let
   # Update spirv-headers rev in lockstep according to DEPs file
-  version = "2019.1";
+  version = "2019.3";
 in
 
-assert version == spirv-headers.version;
 stdenv.mkDerivation rec {
   name = "spirv-tools-${version}";
   inherit version;
@@ -13,11 +12,11 @@ stdenv.mkDerivation rec {
     owner = "KhronosGroup";
     repo = "SPIRV-Tools";
     rev = "v${version}";
-    sha256 = "0vddjzhkrhrm3l3i57nxmq2smv3r1s0ka5ff2kziaahr4hqb479r";
+    sha256 = "1wvipjcjsi815ls08s3dz9hwlbb59dbl4syxkskg1k9d5jjph1a8";
   };
   enableParallelBuilding = true;
 
-  buildInputs = [ cmake python ];
+  buildInputs = [ cmake python3 ];
 
   cmakeFlags = [ "-DSPIRV-Headers_SOURCE_DIR=${spirv-headers.src}" ];
 

From 1ba444e4007c3a14927919051d9bb9692bd23639 Mon Sep 17 00:00:00 2001
From: Manuel Mendez <mmendez534@gmail.com>
Date: Thu, 8 Aug 2019 08:45:52 -0400
Subject: [PATCH 06/27] flent: run through nixfmt

---
 pkgs/applications/networking/flent/default.nix | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index bc0a519a0ee..00522d84569 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,6 +1,5 @@
 { stdenv, buildPythonApplication, fetchFromGitHub, matplotlib, procps, pyqt5
-, sphinx
-}:
+, sphinx }:
 
 buildPythonApplication rec {
   pname = "flent";
@@ -16,15 +15,11 @@ buildPythonApplication rec {
 
   checkInputs = [ procps ];
 
-  propagatedBuildInputs = [
-    matplotlib
-    procps
-    pyqt5
-  ];
+  propagatedBuildInputs = [ matplotlib procps pyqt5 ];
 
   meta = with stdenv.lib; {
     description = "The FLExible Network Tester";
-    homepage = https://flent.org;
+    homepage = "https://flent.org";
     license = licenses.gpl3;
 
     maintainers = [ maintainers.mmlb ];

From a88232c31ae733a5bc148175ea20549cc81e23b2 Mon Sep 17 00:00:00 2001
From: Manuel Mendez <mmendez534@gmail.com>
Date: Thu, 8 Aug 2019 08:51:44 -0400
Subject: [PATCH 07/27] flent: use fetchPypi

---
 pkgs/applications/networking/flent/default.nix | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index 00522d84569..ed7e8ae9d6a 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,14 +1,12 @@
-{ stdenv, buildPythonApplication, fetchFromGitHub, matplotlib, procps, pyqt5
+{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5
 , sphinx }:
 
 buildPythonApplication rec {
   pname = "flent";
   version = "1.2.2";
-  src = fetchFromGitHub {
-    owner = "tohojo";
-    repo = "flent";
-    rev = "v${version}";
-    sha256 = "1llcdakk0nk9xlpjjz7mv4a80yq4sjnbqhaqvyj9m6lbcxgssh2r";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0ziblk36rzr99pbi7xzzkci3sr41m0jf72v38ynp63df6szbbfjb";
   };
 
   buildInputs = [ sphinx ];

From a48c4843cd228f041dc75a120cbfa216e9a2f66a Mon Sep 17 00:00:00 2001
From: Manuel Mendez <mmendez534@gmail.com>
Date: Thu, 8 Aug 2019 08:57:04 -0400
Subject: [PATCH 08/27] flent: use wrapQtAppsHook

---
 pkgs/applications/networking/flent/default.nix | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index ed7e8ae9d6a..9b170735dcf 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5
+{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5, qt5
 , sphinx }:
 
 buildPythonApplication rec {
@@ -10,11 +10,18 @@ buildPythonApplication rec {
   };
 
   buildInputs = [ sphinx ];
+  nativeBuildInputs = [ qt5.wrapQtAppsHook ];
 
   checkInputs = [ procps ];
 
   propagatedBuildInputs = [ matplotlib procps pyqt5 ];
 
+  postInstall = ''
+    for program in $out/bin/*; do
+      wrapQtApp $program --prefix PYTHONPATH : $PYTHONPATH
+    done
+  '';
+
   meta = with stdenv.lib; {
     description = "The FLExible Network Tester";
     homepage = "https://flent.org";

From 170caa4506fe40ebbbc47be62934161d2d6c0bb7 Mon Sep 17 00:00:00 2001
From: Manuel Mendez <mmendez534@gmail.com>
Date: Thu, 8 Aug 2019 09:03:41 -0400
Subject: [PATCH 09/27] flent: 1.2.2 -> 1.3.0

---
 .../applications/networking/flent/default.nix | 23 +++++++++++++------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/pkgs/applications/networking/flent/default.nix b/pkgs/applications/networking/flent/default.nix
index 9b170735dcf..bbd9a7601ac 100644
--- a/pkgs/applications/networking/flent/default.nix
+++ b/pkgs/applications/networking/flent/default.nix
@@ -1,20 +1,29 @@
-{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5, qt5
-, sphinx }:
+{ stdenv, buildPythonApplication, fetchPypi, matplotlib, procps, pyqt5, python
+, pythonPackages, qt5, sphinx, xvfb_run }:
 
 buildPythonApplication rec {
   pname = "flent";
-  version = "1.2.2";
+  version = "1.3.0";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0ziblk36rzr99pbi7xzzkci3sr41m0jf72v38ynp63df6szbbfjb";
+    sha256 = "099779i0ghjd9ikq77z6m6scnlmk946lw9issrgz8zm7babiw4d7";
   };
 
   buildInputs = [ sphinx ];
   nativeBuildInputs = [ qt5.wrapQtAppsHook ];
-
-  checkInputs = [ procps ];
-
   propagatedBuildInputs = [ matplotlib procps pyqt5 ];
+  checkInputs = [ procps pythonPackages.mock pyqt5 xvfb_run ];
+
+  checkPhase = ''
+    cat >test-runner <<EOF
+    #!/bin/sh
+
+    ${python.pythonForBuild.interpreter} nix_run_setup test
+    EOF
+    chmod +x test-runner
+    wrapQtApp test-runner --prefix PYTHONPATH : $PYTHONPATH
+    xvfb-run -s '-screen 0 800x600x24' ./test-runner
+  '';
 
   postInstall = ''
     for program in $out/bin/*; do

From 70462081318239197781d2585013b34fd18ff579 Mon Sep 17 00:00:00 2001
From: Lily Ballard <lily@sb.org>
Date: Tue, 27 Aug 2019 11:27:03 -0700
Subject: [PATCH 10/27] cocoapods-beta: 1.8.0.beta.1 -> 1.8.0.beta.2

---
 .../mobile/cocoapods/Gemfile-beta.lock         | 13 +++++++------
 .../mobile/cocoapods/gemset-beta.nix           | 18 +++++++++---------
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
index 2ddffbf16b7..c75dc334ebc 100644
--- a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
+++ b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    CFPropertyList (3.0.0)
+    CFPropertyList (3.0.1)
     activesupport (4.2.11.1)
       i18n (~> 0.7)
       minitest (~> 5.1)
@@ -12,16 +12,16 @@ GEM
       json (>= 1.5.1)
     atomos (0.1.3)
     claide (1.0.3)
-    cocoapods (1.8.0.beta.1)
+    cocoapods (1.8.0.beta.2)
       activesupport (>= 4.0.2, < 5)
       claide (>= 1.0.2, < 2.0)
-      cocoapods-core (= 1.8.0.beta.1)
+      cocoapods-core (= 1.8.0.beta.2)
       cocoapods-deintegrate (>= 1.0.3, < 2.0)
       cocoapods-downloader (>= 1.2.2, < 2.0)
       cocoapods-plugins (>= 1.0.0, < 2.0)
       cocoapods-search (>= 1.0.0, < 2.0)
       cocoapods-stats (>= 1.0.0, < 2.0)
-      cocoapods-trunk (>= 1.3.1, < 2.0)
+      cocoapods-trunk (>= 1.4.0, < 2.0)
       cocoapods-try (>= 1.1.0, < 2.0)
       colored2 (~> 3.1)
       escape (~> 0.0.4)
@@ -31,9 +31,10 @@ GEM
       nap (~> 1.0)
       ruby-macho (~> 1.4)
       xcodeproj (>= 1.11.1, < 2.0)
-    cocoapods-core (1.8.0.beta.1)
+    cocoapods-core (1.8.0.beta.2)
       activesupport (>= 4.0.2, < 6)
       algoliasearch (~> 1.0)
+      concurrent-ruby (~> 1.0)
       fuzzy_match (~> 2.0.4)
       nap (~> 1.0)
     cocoapods-deintegrate (1.0.4)
@@ -42,7 +43,7 @@ GEM
       nap
     cocoapods-search (1.0.0)
     cocoapods-stats (1.1.0)
-    cocoapods-trunk (1.3.1)
+    cocoapods-trunk (1.4.0)
       nap (>= 0.8, < 2.0)
       netrc (~> 0.11)
     cocoapods-try (1.1.0)
diff --git a/pkgs/development/mobile/cocoapods/gemset-beta.nix b/pkgs/development/mobile/cocoapods/gemset-beta.nix
index baa4748fb94..e2d4127ae44 100644
--- a/pkgs/development/mobile/cocoapods/gemset-beta.nix
+++ b/pkgs/development/mobile/cocoapods/gemset-beta.nix
@@ -36,10 +36,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0ykjag3k5msz3sf1j91rb55da2xh596y06m3a4yl79fiy2id0w9z";
+      sha256 = "0fr8sdzs2q1969zqh790w223hjidlwx4hfm4c91gj0va5j5pv3n8";
       type = "gem";
     };
-    version = "3.0.0";
+    version = "3.0.1";
   };
   claide = {
     groups = ["default"];
@@ -57,21 +57,21 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1gs9ybf1zbajhsn591dwh2papj0bs1dzbnw8shbsm4mfqz976y54";
+      sha256 = "1qsj34czqsy93w2bnwhdhr0cyzjwl7vy3sknmak4syyni6m0rlli";
       type = "gem";
     };
-    version = "1.8.0.beta.1";
+    version = "1.8.0.beta.2";
   };
   cocoapods-core = {
-    dependencies = ["activesupport" "algoliasearch" "fuzzy_match" "nap"];
+    dependencies = ["activesupport" "algoliasearch" "concurrent-ruby" "fuzzy_match" "nap"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "02c0415b7iridf0gypajm4i3vqpq8zs6vx8bw49rm70l554jp14j";
+      sha256 = "166pr9m3da9hsra9rviaxz3i4spm7kl003mkn7sn25r9smcvfdj4";
       type = "gem";
     };
-    version = "1.8.0.beta.1";
+    version = "1.8.0.beta.2";
   };
   cocoapods-deintegrate = {
     groups = ["default"];
@@ -130,10 +130,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1plssgabdv6hcaq1c3gf43kf1d2prx883q8lzdr6chi5byzzs3yl";
+      sha256 = "1m0p27aij7d0n0b8h7nvyv3q3prcpwisbj7sla0fp2hvn4lqarl5";
       type = "gem";
     };
-    version = "1.3.1";
+    version = "1.4.0";
   };
   cocoapods-try = {
     groups = ["default"];

From 93a27dbe9f4c3689e4b62089be1a7d5e7eb6a8aa Mon Sep 17 00:00:00 2001
From: Elis Hirwing <elis@hirwing.se>
Date: Fri, 30 Aug 2019 13:50:50 +0200
Subject: [PATCH 11/27] usbtop: init at 1.0

---
 pkgs/os-specific/linux/usbtop/default.nix | 26 +++++++++++++++++++++++
 pkgs/top-level/all-packages.nix           |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/os-specific/linux/usbtop/default.nix

diff --git a/pkgs/os-specific/linux/usbtop/default.nix b/pkgs/os-specific/linux/usbtop/default.nix
new file mode 100644
index 00000000000..0ff8fcf0ddf
--- /dev/null
+++ b/pkgs/os-specific/linux/usbtop/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub
+, cmake
+, libpcap, boost }:
+
+stdenv.mkDerivation rec {
+  pname = "usbtop";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "aguinet";
+    repo = pname;
+    rev = "release-${version}";
+    sha256 = "0qbad0aq6j4jrh90l6a0akk71wdzhyzmy6q8wl138axyj2bp9kss";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libpcap boost ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/aguinet/usbtop";
+    description = "A top utility that shows an estimated instantaneous bandwidth on USB buses and devices";
+    maintainers = with maintainers; [ etu ];
+    license = licenses.bsd3;
+    platforms = platforms.linux;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6c3af89bc8d..14318795a7b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16494,6 +16494,8 @@ in
     withGui = false;
   };
 
+  usbtop = callPackage ../os-specific/linux/usbtop { };
+
   usbutils = callPackage ../os-specific/linux/usbutils { };
 
   usermount = callPackage ../os-specific/linux/usermount { };

From aacf9235d842ef52daf43ee7ac36be9ca9fbe226 Mon Sep 17 00:00:00 2001
From: Elis Hirwing <elis@hirwing.se>
Date: Fri, 30 Aug 2019 13:51:10 +0200
Subject: [PATCH 12/27] nixos/usbtop: Add module to install usbtop and to
 enable kernel module

---
 nixos/modules/module-list.nix     |  1 +
 nixos/modules/programs/usbtop.nix | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 nixos/modules/programs/usbtop.nix

diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
index 75df6c8d453..fc03d05b07d 100644
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@@ -152,6 +152,7 @@
   ./programs/tmux.nix
   ./programs/tsm-client.nix
   ./programs/udevil.nix
+  ./programs/usbtop.nix
   ./programs/venus.nix
   ./programs/vim.nix
   ./programs/wavemon.nix
diff --git a/nixos/modules/programs/usbtop.nix b/nixos/modules/programs/usbtop.nix
new file mode 100644
index 00000000000..c1b6ee38caa
--- /dev/null
+++ b/nixos/modules/programs/usbtop.nix
@@ -0,0 +1,21 @@
+{ config, pkgs, lib, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.usbtop;
+in {
+  options = {
+    programs.usbtop.enable = mkEnableOption "usbtop and required kernel module";
+  };
+
+  config = mkIf cfg.enable {
+    environment.systemPackages = with pkgs; [
+      usbtop
+    ];
+
+    boot.kernelModules = [
+      "usbmon"
+    ];
+  };
+}

From 3cd8f4300c1b3e5402c7431fbed504ff0f9d6d1c Mon Sep 17 00:00:00 2001
From: Averell Dalton <averell+nixpkgs@rxd4.com>
Date: Mon, 22 Jul 2019 23:39:35 +0200
Subject: [PATCH 13/27] perlPackages.ConfigSimple: init at 4.59

---
 pkgs/top-level/perl-packages.nix | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 6180f6372e2..442df5ec715 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -2879,6 +2879,18 @@ let
     };
   };
 
+  ConfigSimple = buildPerlPackage {
+    pname = "Config-Simple";
+    version = "4.59";
+    src = fetchurl {
+      url = mirror://cpan/authors/id/S/SH/SHERZODR/Config-Simple-4.59.tar.gz;
+      sha256 = "0m0hg29baarw5ds768q9r4rxb27im8kj4fazyf9gjqw4mmssjy6b";
+    };
+    meta = {
+      description = "Simple configuration file class";
+    };
+  };
+
   ConfigStd = buildPerlModule {
     pname = "Config-Std";
     version = "0.903";

From 1eb8f58130ff2524b7a7caa245db81ae309e53f7 Mon Sep 17 00:00:00 2001
From: Averell Dalton <averell+nixpkgs@rxd4.com>
Date: Mon, 5 Aug 2019 18:22:31 +0200
Subject: [PATCH 14/27] x2goserver: init at 4.1.0.3

---
 .../networking/remote/x2goserver/default.nix  | 93 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 95 insertions(+)
 create mode 100644 pkgs/applications/networking/remote/x2goserver/default.nix

diff --git a/pkgs/applications/networking/remote/x2goserver/default.nix b/pkgs/applications/networking/remote/x2goserver/default.nix
new file mode 100644
index 00000000000..f69d2326217
--- /dev/null
+++ b/pkgs/applications/networking/remote/x2goserver/default.nix
@@ -0,0 +1,93 @@
+{ stdenv, lib, fetchurl, perlPackages, makeWrapper, perl, which, nx-libs
+, utillinux, coreutils, glibc, gawk, gnused, gnugrep, findutils, xorg
+, nettools, iproute, bc, procps, psmisc, lsof, pwgen, openssh, sshfs, bash
+}:
+
+let
+  pname = "x2goserver";
+  version = "4.1.0.3";
+
+  src = fetchurl {
+    url = "http://code.x2go.org/releases/source/x2goserver/${pname}-${version}.tar.gz";
+    sha256 = "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7";
+  };
+
+  x2go-perl = perlPackages.buildPerlPackage rec {
+    pname = "X2Go";
+    inherit version src;
+    makeFlags = [ "-f" "Makefile.perl" ];
+    patchPhase = ''
+      substituteInPlace X2Go/Config.pm --replace '/etc/x2go' '/var/lib/x2go/conf'
+      substituteInPlace X2Go/Server/DB.pm \
+        --replace '$x2go_lib_path/libx2go-server-db-sqlite3-wrapper' \
+                  '/run/wrappers/bin/x2gosqliteWrapper'
+      substituteInPlace X2Go/Server/DB/SQLite3.pm --replace "user='x2gouser'" "user='x2go'"
+    '';
+  };
+
+  perlEnv = perl.withPackages (p: with p; [
+    x2go-perl DBI DBDSQLite FileBaseDir TryTiny CaptureTiny ConfigSimple Switch
+  ]);
+
+  binaryDeps = [
+    perlEnv which nx-libs utillinux coreutils glibc.bin gawk gnused gnugrep
+    findutils nettools iproute bc procps psmisc lsof pwgen openssh sshfs
+    xorg.xauth xorg.xinit xorg.xrandr xorg.xmodmap xorg.xwininfo xorg.fontutil
+    xorg.xkbcomp xorg.setxkbmap
+  ];
+in
+stdenv.mkDerivation rec {
+  inherit pname version src;
+
+  buildInputs = [ perlEnv bash ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  prePatch = ''
+    patchShebangs .
+    sed -i '/Makefile.PL\|Makefile.perl/d' Makefile
+    for i in */Makefile; do
+      substituteInPlace "$i" --replace "-o root -g root " ""
+    done
+    substituteInPlace libx2go-server-db-perl/Makefile --replace "chmod 2755" "chmod 755"
+    for i in x2goserver/sbin/x2godbadmin x2goserver/bin/x2go*
+    do
+      substituteInPlace $i --replace '/etc/x2go' '/var/lib/x2go/conf'
+    done
+    substituteInPlace x2goserver/sbin/x2gocleansessions \
+      --replace '/var/run/x2goserver.pid' '/var/run/x2go/x2goserver.pid'
+    substituteInPlace x2goserver/sbin/x2godbadmin --replace 'user="x2gouser"' 'user="x2go"'
+    substituteInPlace x2goserver-xsession/etc/Xsession \
+      --replace "SSH_AGENT /bin/bash -c" "SSH_AGENT ${bash}/bin/bash -c" \
+      --replace "[ -f /etc/redhat-release ]" "[ -d /etc/nix ] || [ -f /etc/redhat-release ]"
+  '';
+
+  makeFlags = [ "PREFIX=/" "NXLIBDIR=${nx-libs}/lib/nx" ];
+
+  installFlags = [ "DESTDIR=$(out)" ];
+
+  postInstall = ''
+    mv $out/etc/x2go/x2goserver.conf{,.example}
+    mv $out/etc/x2go/x2goagent.options{,.example}
+    ln -sf ${nx-libs}/bin/nxagent $out/bin/x2goagent
+    for i in $out/sbin/x2go* $(find $out/bin -type f) \
+      $(ls $out/lib/x2go/x2go* | grep -v x2gocheckport)
+    do
+      wrapProgram $i --prefix PATH : ${lib.makeBinPath binaryDeps}:$out
+    done
+    # We're patching @INC of the setgid wrapper, because we can't mix
+    # the perl wrapper (for PERL5LIB) with security.wrappers (for setgid)
+    sed -ie "s,.\+bin/perl,#!${perl}/bin/perl -I ${perlEnv}/lib/perl5/site_perl," \
+      $out/lib/x2go/libx2go-server-db-sqlite3-wrapper.pl
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Remote desktop application, server component";
+    homepage = "http://x2go.org/";
+    platforms = stdenv.lib.platforms.linux;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.averelld ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 9eeb1084144..3f944f38c66 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21331,6 +21331,8 @@ in
 
   x2goclient = libsForQt5.callPackage ../applications/networking/remote/x2goclient { };
 
+  x2goserver = callPackage ../applications/networking/remote/x2goserver { };
+
   x2vnc = callPackage ../tools/X11/x2vnc { };
 
   x32edit = callPackage ../applications/audio/midas/x32edit.nix {};

From f0d23b63432d7093f55ce2f49c89d60b6cfc455f Mon Sep 17 00:00:00 2001
From: Averell Dalton <averell+nixpkgs@rxd4.com>
Date: Mon, 5 Aug 2019 18:26:14 +0200
Subject: [PATCH 15/27] x2goserver: add module

---
 nixos/modules/module-list.nix         |   1 +
 nixos/modules/programs/x2goserver.nix | 148 ++++++++++++++++++++++++++
 2 files changed, 149 insertions(+)
 create mode 100644 nixos/modules/programs/x2goserver.nix

diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
index 22fd5d7609d..b439602566f 100644
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@@ -158,6 +158,7 @@
   ./programs/way-cooler.nix
   ./programs/waybar.nix
   ./programs/wireshark.nix
+  ./programs/x2goserver.nix
   ./programs/xfs_quota.nix
   ./programs/xonsh.nix
   ./programs/xss-lock.nix
diff --git a/nixos/modules/programs/x2goserver.nix b/nixos/modules/programs/x2goserver.nix
new file mode 100644
index 00000000000..d9e7b6e4a5c
--- /dev/null
+++ b/nixos/modules/programs/x2goserver.nix
@@ -0,0 +1,148 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.x2goserver;
+
+  defaults = {
+    superenicer = { "enable" = cfg.superenicer.enable; };
+  };
+  confText = generators.toINI {} (recursiveUpdate defaults cfg.settings);
+  x2goServerConf = pkgs.writeText "x2goserver.conf" confText;
+
+  x2goAgentOptions = pkgs.writeText "x2goagent.options" ''
+    X2GO_NXOPTIONS=""
+    X2GO_NXAGENT_DEFAULT_OPTIONS="${concatStringsSep " " cfg.nxagentDefaultOptions}"
+  '';
+
+in {
+  options.programs.x2goserver = {
+    enable = mkEnableOption "x2goserver" // {
+      description = ''
+        Enables the x2goserver module.
+        NOTE: This will create a good amount of symlinks in `/usr/local/bin`
+      '';
+    };
+
+    superenicer = {
+      enable = mkEnableOption "superenicer" // {
+        description = ''
+          Enables the SupeReNicer code in x2gocleansessions, this will renice
+          suspended sessions to nice level 19 and renice them to level 0 if the
+          session becomes marked as running again
+        '';
+      };
+    };
+
+    nxagentDefaultOptions = mkOption {
+      type = types.listOf types.str;
+      default = [ "-extension GLX" "-nolisten tcp" ];
+      example = [ "-extension GLX" "-nolisten tcp" ];
+      description = ''
+        List of default nx agent options.
+      '';
+    };
+
+    settings = mkOption {
+      type = types.attrsOf types.attrs;
+      default = {};
+      description = ''
+        x2goserver.conf ini configuration as nix attributes. See
+        `x2goserver.conf(5)` for details
+      '';
+      example = literalExample ''
+        superenicer = {
+          "enable" = "yes";
+          "idle-nice-level" = 19;
+        };
+        telekinesis = { "enable" = "no"; };
+      '';
+    };
+  };
+
+  config = mkIf cfg.enable {
+
+    environment.systemPackages = [ pkgs.x2goserver ];
+
+    users.groups.x2go = {};
+    users.users.x2go = {
+      home = "/var/lib/x2go/db";
+      group = "x2go";
+    };
+
+    security.wrappers.x2gosqliteWrapper = {
+      source = "${pkgs.x2goserver}/lib/x2go/libx2go-server-db-sqlite3-wrapper.pl";
+      owner = "x2go";
+      group = "x2go";
+      setgid = true;
+    };
+    security.wrappers.x2goprintWrapper = {
+      source = "${pkgs.x2goserver}/bin/x2goprint";
+      owner = "x2go";
+      group = "x2go";
+      setgid = true;
+    };
+
+    systemd.tmpfiles.rules = with pkgs; [
+      "d /var/lib/x2go/ - x2go x2go - -"
+      "d /var/lib/x2go/db - x2go x2go - -"
+      "d /var/lib/x2go/conf - x2go x2go - -"
+      "d /run/x2go 0755 x2go x2go - -"
+    ] ++
+    # x2goclient sends SSH commands with preset PATH set to
+    # "/usr/local/bin;/usr/bin;/bin". Since we cannot filter arbitrary ssh
+    # commands, we have to make the following executables available.
+    map (f: "L+ /usr/local/bin/${f} - - - - ${x2goserver}/bin/${f}") [
+      "x2goagent" "x2gobasepath" "x2gocleansessions" "x2gocmdexitmessage"
+      "x2godbadmin" "x2gofeature" "x2gofeaturelist" "x2gofm" "x2gogetapps"
+      "x2gogetservers" "x2golistdesktops" "x2golistmounts" "x2golistsessions"
+      "x2golistsessions_root" "x2golistshadowsessions" "x2gomountdirs"
+      "x2gopath" "x2goprint" "x2goresume-desktopsharing" "x2goresume-session"
+      "x2goruncommand" "x2goserver-run-extensions" "x2gosessionlimit"
+      "x2gosetkeyboard" "x2goshowblocks" "x2gostartagent"
+      "x2gosuspend-desktopsharing" "x2gosuspend-session"
+      "x2goterminate-desktopsharing" "x2goterminate-session"
+      "x2goumount-session" "x2goversion"
+    ] ++ [
+      "L+ /usr/local/bin/awk - - - - ${gawk}/bin/awk"
+      "L+ /usr/local/bin/chmod - - - - ${coreutils}/bin/chmod"
+      "L+ /usr/local/bin/cp - - - - ${coreutils}/bin/cp"
+      "L+ /usr/local/bin/sed - - - - ${gnused}/bin/sed"
+      "L+ /usr/local/bin/setsid - - - - ${utillinux}/bin/setsid"
+      "L+ /usr/local/bin/xrandr - - - - ${xorg.xrandr}/bin/xrandr"
+      "L+ /usr/local/bin/xmodmap - - - - ${xorg.xmodmap}/bin/xmodmap"
+    ];
+
+    systemd.services.x2goserver = {
+      description = "X2Go Server Daemon";
+      wantedBy = [ "multi-user.target" ];
+      unitConfig.Documentation = "man:x2goserver.conf(5)";
+      serviceConfig = {
+        Type = "forking";
+        ExecStart = "${pkgs.x2goserver}/bin/x2gocleansessions";
+        PIDFile = "/run/x2go/x2goserver.pid";
+        User = "x2go";
+        Group = "x2go";
+        RuntimeDirectory = "x2go";
+        StateDirectory = "x2go";
+      };
+      preStart = ''
+        if [ ! -e /var/lib/x2go/setup_ran ]
+        then
+          mkdir -p /var/lib/x2go/conf
+          cp -r ${pkgs.x2goserver}/etc/x2go/* /var/lib/x2go/conf/
+          ln -sf ${x2goServerConf} /var/lib/x2go/conf/x2goserver.conf
+          ln -sf ${x2goAgentOptions} /var/lib/x2go/conf/x2goagent.options
+          ${pkgs.x2goserver}/bin/x2godbadmin --createdb
+          touch /var/lib/x2go/setup_ran
+        fi
+      '';
+    };
+
+    # https://bugs.x2go.org/cgi-bin/bugreport.cgi?bug=276
+    security.sudo.extraConfig = ''
+      Defaults  env_keep+=QT_GRAPHICSSYSTEM
+    '';
+  };
+}

From 72f711eadaf18315adc1188a9c1b2198713b8ae4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=C3=ABl=20de=20Kok?= <me@danieldk.eu>
Date: Sat, 31 Aug 2019 07:36:28 +0200
Subject: [PATCH 16/27] maturin: 0.7.0 -> 0.7.1

Change:

- maturin build --interpreter/maturin publish --interpreter builds
  only a source distribution.
---
 pkgs/development/tools/rust/maturin/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/tools/rust/maturin/default.nix b/pkgs/development/tools/rust/maturin/default.nix
index 4b07129ae0e..7bd49132d0e 100644
--- a/pkgs/development/tools/rust/maturin/default.nix
+++ b/pkgs/development/tools/rust/maturin/default.nix
@@ -5,16 +5,16 @@ let
   inherit (darwin.apple_sdk.frameworks) Security;
 in rustPlatform.buildRustPackage rec {
   name = "maturin-${version}";
-  version = "0.7.0";
+  version = "0.7.1";
 
   src = fetchFromGitHub {
     owner = "PyO3";
     repo = "maturin";
     rev = "v${version}";
-    sha256 = "1qscn8ycyg9ldkp1v5178mlw8r5ak2p12x52c0w4hgij7y1q5s39";
+    sha256 = "0srsb305gld6zmz7qm5zk4gawqqlywdpray04z8xcij146mccci2";
   };
 
-  cargoSha256 = "0fk9dgwkgkkmxxd8ydl0vp14jhzi65pkz36v5h3nkp4cb4n4cvdj";
+  cargoSha256 = "0bscwbrzjaps4yqcrqhan56kdmh0n014w4ldsbv3sbhpw5izz335";
 
   nativeBuildInputs = [ pkgconfig ];
 

From c3c8f17439bc3aa4313c1137f99c3160b60825c4 Mon Sep 17 00:00:00 2001
From: Danielle Lancashire <dani@builds.terrible.systems>
Date: Sat, 31 Aug 2019 10:08:48 +0200
Subject: [PATCH 17/27] maintainers: add endocrimes

---
 maintainers/maintainer-list.nix | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index f5c00ff6268..f67bd770f74 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -1822,6 +1822,12 @@
     githubId = 18535642;
     name = "Emily";
   };
+  endocrimes = {
+    email = "dani@builds.terrible.systems";
+    github = "endocrimes";
+    githubId = 1330683;
+    name = "Danielle Lancashire";
+  };
   ederoyd46 = {
     email = "matt@ederoyd.co.uk";
     github = "ederoyd46";

From 1c9253ce2b512bbe625a6fafbae58228498f42fb Mon Sep 17 00:00:00 2001
From: Danielle Lancashire <dani@builds.terrible.systems>
Date: Sat, 31 Aug 2019 10:09:32 +0200
Subject: [PATCH 18/27] gotestsum: Init at 0.3.5

---
 pkgs/development/tools/gotestsum/default.nix | 23 ++++++++++++++++++++
 pkgs/top-level/all-packages.nix              |  2 ++
 2 files changed, 25 insertions(+)
 create mode 100644 pkgs/development/tools/gotestsum/default.nix

diff --git a/pkgs/development/tools/gotestsum/default.nix b/pkgs/development/tools/gotestsum/default.nix
new file mode 100644
index 00000000000..36e41bddf25
--- /dev/null
+++ b/pkgs/development/tools/gotestsum/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, fetchFromGitHub, buildGoModule }:
+
+buildGoModule rec {
+  pname = "gotestsum";
+  version = "0.3.5";
+
+  src = fetchFromGitHub {
+    owner = "gotestyourself";
+    repo = "gotestsum";
+    rev = "v${version}";
+    sha256 = "1d4sbvk9wqzl3g3da8inqdkvd43rkwvmq969jlgl1k1agv5xjxqv";
+  };
+
+  modSha256 = "1dgs643pmcw68yc003zss52hbvsy6hxzwkrhr0qmsqkmzxryb3bn";
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/gotestyourself/gotestsum";
+    description = "A human friendly `go test` runner";
+    platforms = platforms.linux ++ platforms.darwin;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ endocrimes ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1f996f185d2..39caf0596fe 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16198,6 +16198,8 @@ in
 
   gotests = callPackage ../development/tools/gotests { };
 
+  gotestsum = callPackage ../development/tools/gotestsum { };
+
   impl = callPackage ../development/tools/impl { };
 
   quicktemplate = callPackage ../development/tools/quicktemplate { };

From 661b311057ae4713f1f473659361961e86bad155 Mon Sep 17 00:00:00 2001
From: Tadeo Kondrak <me@tadeo.ca>
Date: Fri, 30 Aug 2019 21:36:57 -0600
Subject: [PATCH 19/27] discord-canary: 0.0.93 -> 0.0.95

---
 .../networking/instant-messengers/discord/default.nix       | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/networking/instant-messengers/discord/default.nix b/pkgs/applications/networking/instant-messengers/discord/default.nix
index 189092a6d5e..1d9d645b0ed 100644
--- a/pkgs/applications/networking/instant-messengers/discord/default.nix
+++ b/pkgs/applications/networking/instant-messengers/discord/default.nix
@@ -27,10 +27,10 @@ in {
     pname = "discord-canary";
     binaryName = "DiscordCanary";
     desktopName = "Discord Canary";
-    version = "0.0.93";
+    version = "0.0.95";
     src = fetchurl {
-      url = "https://dl-canary.discordapp.net/apps/linux/0.0.93/discord-canary-0.0.93.tar.gz";
-      sha256 = "1jzm5fm7a1p68ims7bv5am0bpbvrhbynzblpj9qrzzrwakdaywbi";
+      url = "https://dl-canary.discordapp.net/apps/linux/0.0.95/discord-canary-0.0.95.tar.gz";
+      sha256 = "06qhm73kc88pq0lgbi7qjy4gx9ighkmx128fdm1dpzfv62fjdasw";
     };
   };
 }.${branch}

From a8aeb913b075f85c67b552620b06c3bb577fe5ea Mon Sep 17 00:00:00 2001
From: Kevin Quick <kquick@galois.com>
Date: Fri, 30 Aug 2019 23:28:26 -0700
Subject: [PATCH 20/27] python: thespian: 3.9.9 -> 3.9.10

---
 pkgs/development/python-modules/thespian/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/thespian/default.nix b/pkgs/development/python-modules/thespian/default.nix
index cd4a30f656a..f4c498bed95 100644
--- a/pkgs/development/python-modules/thespian/default.nix
+++ b/pkgs/development/python-modules/thespian/default.nix
@@ -1,13 +1,13 @@
 { fetchPypi, buildPythonPackage, lib }:
 
 buildPythonPackage rec {
-  version = "3.9.9";
+  version = "3.9.10";
   pname = "thespian";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "c89e1973465feb88b694f3884d24723932a6b0e4df8d909f61e44ff371af7380";
+    sha256 = "bffb04b93afcbab0268332445f02757c326f95056eb7e1e2f0515c1dfb92ac7d";
   };
 
   # Do not run the test suite: it takes a long time and uses

From 35ac3344e747e61abcf1847add8d76a6a2812e8a Mon Sep 17 00:00:00 2001
From: Alexander <lebastr@gmail.com>
Date: Sat, 31 Aug 2019 15:06:46 +0300
Subject: [PATCH 21/27] colmap: init at 3.5 (#67759)

* colmap: init at 3.5
---
 .../science/misc/colmap/default.nix           | 37 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  3 ++
 2 files changed, 40 insertions(+)
 create mode 100644 pkgs/applications/science/misc/colmap/default.nix

diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix
new file mode 100644
index 00000000000..672569ed100
--- /dev/null
+++ b/pkgs/applications/science/misc/colmap/default.nix
@@ -0,0 +1,37 @@
+{ mkDerivation, lib, fetchFromGitHub, cmake, boost, ceres-solver, eigen,
+  freeimage, glog, libGLU, glew, qtbase,
+  cudaSupport ? false, cudatoolkit ? null }:
+
+assert !cudaSupport || cudatoolkit != null;
+
+let boost_static = boost.override { enableStatic = true; };
+in 
+mkDerivation rec {
+  version = "3.5";
+  pname = "colmap";
+  src = fetchFromGitHub {
+     owner = "colmap";
+     repo = "colmap";
+     rev = version;
+     sha256 = "1vnb62p0y2bnga173wmjs0lnyqdjikv0fkcxjzxm8187khk2lly8";
+  };
+  
+  buildInputs = [
+    boost_static ceres-solver eigen
+    freeimage glog libGLU glew qtbase
+  ] ++ lib.optional cudaSupport cudatoolkit;
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = "COLMAP - Structure-From-Motion and Multi-View Stereo pipeline";
+    longDescription = ''
+       COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline
+       with a graphical and command-line interface.
+    '';
+    homepage = https://colmap.github.io/index.html;
+    license = licenses.bsd2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ lebastr ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 4d0a21b95e4..ee3a4f7d68e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -7377,6 +7377,9 @@ in
 
   colm = callPackage ../development/compilers/colm { };
 
+  colmap = libsForQt5.callPackage ../applications/science/misc/colmap { };
+  colmapWithCuda = colmap.override { cudaSupport = true; };
+
   chickenPackages_4 = callPackage ../development/compilers/chicken/4 { };
   chickenPackages_5 = callPackage ../development/compilers/chicken/5 { };
   chickenPackages = chickenPackages_5;

From ccf6d84366cb2ba946c6a0c2914fa9a473bd54e8 Mon Sep 17 00:00:00 2001
From: Benjamin Staffin <benley@gmail.com>
Date: Sat, 31 Aug 2019 08:14:46 -0400
Subject: [PATCH 22/27] yubioath-desktop: Fix desktop launcher icon (#67793)

---
 pkgs/applications/misc/yubioath-desktop/default.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/applications/misc/yubioath-desktop/default.nix b/pkgs/applications/misc/yubioath-desktop/default.nix
index 843bc0c1c23..d7a019c1c41 100644
--- a/pkgs/applications/misc/yubioath-desktop/default.nix
+++ b/pkgs/applications/misc/yubioath-desktop/default.nix
@@ -44,6 +44,7 @@ mkDerivation rec {
       cp resources/icons/*.{icns,ico,png,xpm} $out/share/yubioath/icons
       substituteInPlace $out/share/applications/yubioath-desktop.desktop \
         --replace 'Exec=yubioath-desktop' "Exec=$out/bin/yubioath-desktop" \
+        --replace 'Icon=yubioath' "Icon=$out/share/yubioath/icons/yubioath.png"
   '';
 
   meta = with stdenv.lib; {

From 107af97c9090cf0d0722889553fcc3ffc45b22ac Mon Sep 17 00:00:00 2001
From: Peter Simons <simons@cryp.to>
Date: Sat, 31 Aug 2019 14:45:33 +0200
Subject: [PATCH 23/27] python-mailman-hyperkitty: initial version 1.1.0

---
 .../mailman-hyperkitty/default.nix            | 26 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/development/python-modules/mailman-hyperkitty/default.nix

diff --git a/pkgs/development/python-modules/mailman-hyperkitty/default.nix b/pkgs/development/python-modules/mailman-hyperkitty/default.nix
new file mode 100644
index 00000000000..fd89260ab94
--- /dev/null
+++ b/pkgs/development/python-modules/mailman-hyperkitty/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, buildPythonPackage, fetchPypi, mailman, mock }:
+
+buildPythonPackage rec {
+  pname = "mailman-hyperkitty";
+  version = "1.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1lfqa9admhvdv71f528jmz2wl0i5cv77v6l64px2pm4zqr9ckkjx";
+  };
+
+  propagatedBuildInputs = [ mailman ];
+  checkInputs = [ mock ];
+
+  checkPhase = ''
+    python -m nose2 -v
+  '';
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Mailman archiver plugin for HyperKitty";
+    homepage = https://gitlab.com/mailman/mailman-hyperkitty;
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ globin peti ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 9099552add2..8eaf7cd0ae8 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -717,6 +717,8 @@ in {
 
   mailmanclient = callPackage ../development/python-modules/mailmanclient { };
 
+  mailman-hyperkitty = callPackage ../development/python-modules/mailman-hyperkitty { };
+
   manhole = callPackage ../development/python-modules/manhole { };
 
   markerlib = callPackage ../development/python-modules/markerlib { };

From a919868ff14a65ad40319b1cfe5100c0cc0f85ec Mon Sep 17 00:00:00 2001
From: Tim Steinbach <tim@nequissimus.com>
Date: Sat, 31 Aug 2019 09:17:48 -0400
Subject: [PATCH 24/27] linux: Remove 5.1

The 5.1.x series is not supported anymore
---
 pkgs/os-specific/linux/kernel/linux-5.1.nix | 18 ------------------
 pkgs/top-level/all-packages.nix             |  9 ---------
 2 files changed, 27 deletions(-)
 delete mode 100644 pkgs/os-specific/linux/kernel/linux-5.1.nix

diff --git a/pkgs/os-specific/linux/kernel/linux-5.1.nix b/pkgs/os-specific/linux/kernel/linux-5.1.nix
deleted file mode 100644
index ad3b292656e..00000000000
--- a/pkgs/os-specific/linux/kernel/linux-5.1.nix
+++ /dev/null
@@ -1,18 +0,0 @@
-{ stdenv, buildPackages, fetchurl, perl, buildLinux, modDirVersionArg ? null, ... } @ args:
-
-with stdenv.lib;
-
-buildLinux (args // rec {
-  version = "5.1.21";
-
-  # modDirVersion needs to be x.y.z, will automatically add .0 if needed
-  modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg;
-
-  # branchVersion needs to be x.y
-  extraMeta.branch = concatStrings (intersperse "." (take 2 (splitString "." version)));
-
-  src = fetchurl {
-    url = "mirror://kernel/linux/kernel/v5.x/linux-${version}.tar.xz";
-    sha256 = "1xj1wfhjz2s5a8j6zx3fsd7rrrkvw5waszzylf2gn3ag6615yjan";
-  };
-} // (args.argsOverride or {}))
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ee3a4f7d68e..e23691b9b89 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15743,14 +15743,6 @@ in
       ];
   };
 
-  linux_5_1 = callPackage ../os-specific/linux/kernel/linux-5.1.nix {
-    kernelPatches =
-      [ kernelPatches.bridge_stp_helper
-        kernelPatches.modinst_arg_list_too_long
-        kernelPatches.export_kernel_fpu_functions
-      ];
-  };
-
   linux_5_2 = callPackage ../os-specific/linux/kernel/linux-5.2.nix {
     kernelPatches =
       [ kernelPatches.bridge_stp_helper
@@ -15961,7 +15953,6 @@ in
   linuxPackages_4_9 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_9);
   linuxPackages_4_14 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_14);
   linuxPackages_4_19 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_19);
-  linuxPackages_5_1 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_5_1);
   linuxPackages_5_2 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_5_2);
 
   # When adding to this list:

From 1da1a7a4794de78db9461e094de0b5dd312cbe41 Mon Sep 17 00:00:00 2001
From: Alyssa Ross <hi@alyssa.is>
Date: Thu, 4 Jul 2019 00:23:31 +0000
Subject: [PATCH 25/27] pari: 2.11.1 -> 2.11.2

---
 pkgs/applications/science/math/pari/default.nix | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 72827112c50..89ae354e7c7 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -1,6 +1,5 @@
 { stdenv
 , fetchurl
-, fetchpatch
 , gmp
 , readline
 , libX11
@@ -13,25 +12,13 @@ assert withThread -> libpthreadstubs != null;
 
 stdenv.mkDerivation rec {
   pname = "pari";
-  version = "2.11.1";
+  version = "2.11.2";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz";
-    sha256 = "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94";
+    sha256 = "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa";
   };
 
-  patches = [
-    # Fix a off-by-one bug that can potentially lead to segfaults (accepted upstream)
-    # https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2117
-    # https://trac.sagemath.org/ticket/27335
-    (fetchpatch {
-      name = "fix-off-by-one-error.patch";
-      # only relevant parts of https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=patch;h=aa1ee6e0898d177e6bcf49237d82c804bc410985
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pari/patches/red_montgomery.patch?id=bbea55c96e1f05302b3c7f593cf64492497047c5";
-      sha256 = "0vqkmhgv9splsdswp6zjnkj50z76rc1m6k9iy3cf9dxwqw3h3nr6";
-    })
-  ];
-
   buildInputs = [
     gmp
     readline

From c4adeddb5f8e945517068968d06ea838b7c24bd3 Mon Sep 17 00:00:00 2001
From: Averell Dalton <averell+nixpkgs@rxd4.com>
Date: Wed, 7 Aug 2019 21:30:58 +0200
Subject: [PATCH 26/27] opencv: dont try cuda on 32 bit

config.cudaSupport can be true and cudatoolkit doesn't work with i686,
which can happen inside pkgsi686Linux wrapping.
---
 pkgs/development/libraries/opencv/3.x.nix | 3 ++-
 pkgs/development/libraries/opencv/4.x.nix | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/libraries/opencv/3.x.nix b/pkgs/development/libraries/opencv/3.x.nix
index d5dc716c4a8..34615f44eb4 100644
--- a/pkgs/development/libraries/opencv/3.x.nix
+++ b/pkgs/development/libraries/opencv/3.x.nix
@@ -14,7 +14,8 @@
 , enableOpenblas  ? true, openblas
 , enableContrib   ? true
 
-, enableCuda      ? config.cudaSupport or false, cudatoolkit
+, enableCuda      ? (config.cudaSupport or false) &&
+                    stdenv.hostPlatform.isx86_64, cudatoolkit
 
 , enableUnfree    ? false
 , enableIpp       ? false
diff --git a/pkgs/development/libraries/opencv/4.x.nix b/pkgs/development/libraries/opencv/4.x.nix
index 3fdc392e92b..44bd9c32aef 100644
--- a/pkgs/development/libraries/opencv/4.x.nix
+++ b/pkgs/development/libraries/opencv/4.x.nix
@@ -14,7 +14,8 @@
 , enableOpenblas  ? true, openblas
 , enableContrib   ? true
 
-, enableCuda      ? config.cudaSupport or false, cudatoolkit
+, enableCuda      ? (config.cudaSupport or false) &&
+                    stdenv.hostPlatform.isx86_64, cudatoolkit
 
 , enableUnfree    ? false
 , enableIpp       ? false

From cbbe9f0f211a7c96e7daa7a6e9242b46f841fff2 Mon Sep 17 00:00:00 2001
From: edef <edef@edef.eu>
Date: Sat, 31 Aug 2019 15:56:10 +0000
Subject: [PATCH 27/27] patchutils: add perl to buildInputs

This was silently producing perl scripts with empty shebang lines,
breaking a bunch of the binaries.
---
 pkgs/tools/text/patchutils/generic.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/tools/text/patchutils/generic.nix b/pkgs/tools/text/patchutils/generic.nix
index 87d925e333f..9d7ac4b53f0 100644
--- a/pkgs/tools/text/patchutils/generic.nix
+++ b/pkgs/tools/text/patchutils/generic.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl
+{ stdenv, fetchurl, perl
 , version, sha256, patches ? []
 , ...
 }:
@@ -11,6 +11,7 @@ stdenv.mkDerivation rec {
     inherit sha256;
   };
 
+  buildInputs = [ perl ];
   hardeningDisable = [ "format" ];
 
   doCheck = false; # fails