Merge master into staging-next

18 files changed, 871 insertions, 127 deletions

diff --git a/pkgs/applications/altcoins/wownero.nix b/pkgs/applications/altcoins/wownero.nix
index 4b62ba759f36..fdf2c739ac6f 100644
--- a/pkgs/applications/altcoins/wownero.nix
+++ b/pkgs/applications/altcoins/wownero.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, cmake, pkgconfig, git
-, boost, miniupnpc, openssl, unbound, cppzmq
-, zeromq, pcsclite, readline, libsodium
+, boost, miniupnpc_2, openssl, unbound, cppzmq
+, zeromq, pcsclite, readline, libsodium, rapidjson
 , CoreData, IOKit, PCSC
 }:
 
@@ -11,19 +11,18 @@ with stdenv.lib;
 stdenv.mkDerivation rec {
   name = "wownero-${version}";
 
-  version = "0.4.0.0";
+  version = "0.5.0.0";
   src = fetchFromGitHub {
     owner = "wownero";
     repo = "wownero";
-    fetchSubmodules = true;
     rev    = "v${version}";
-    sha256 = "1z5fpl4gwys4v8ffrymlzwrbnrbg73x553a9lxwny7ba8yg2k14p";
+    sha256 = "1dy9ycabva2z0896al1k2avl9xppkxvm1p2jwmg509ahjl98k3sy";
   };
 
   nativeBuildInputs = [ cmake pkgconfig git ];
 
   buildInputs = [
-    boost miniupnpc openssl unbound
+    boost miniupnpc_2 openssl unbound rapidjson
     cppzmq zeromq pcsclite readline libsodium
   ] ++ optionals stdenv.isDarwin [ IOKit CoreData PCSC ];
 
diff --git a/pkgs/applications/editors/dit/default.nix b/pkgs/applications/editors/dit/default.nix
index 33d80a577dbe..12ca7a071406 100644
--- a/pkgs/applications/editors/dit/default.nix
+++ b/pkgs/applications/editors/dit/default.nix
@@ -1,22 +1,20 @@
-{ fetchurl, stdenv, coreutils, ncurses, lua }:
+{ lib, fetchurl, stdenv, libiconv, ncurses, lua }:
 
 stdenv.mkDerivation rec {
   name = "dit-${version}";
-  version = "0.4";
+  version = "0.5";
 
   src = fetchurl {
     url = "https://hisham.hm/dit/releases/${version}/${name}.tar.gz";
-    sha256 = "0bwczbv7annbbpg7bgbsqd5kwypn81sza4v7v99fin94wwmcn784";
+    sha256 = "05vhr1gl3bb5fg49v84xhmjaqdjw6djampvylw10ydvbpnpvjvjc";
   };
 
-  buildInputs = [ coreutils ncurses lua ];
+  buildInputs = [ ncurses lua ]
+    ++ lib.optional stdenv.isDarwin libiconv;
 
+  # fix paths
   prePatch = ''
     patchShebangs tools/GenHeaders
-  '';
-
-  # needs GNU tail for tail -r
-  postPatch = ''
     substituteInPlace Prototypes.h --replace 'tail' "$(type -P tail)"
   '';
 
diff --git a/pkgs/applications/editors/emacs/macport.nix b/pkgs/applications/editors/emacs/macport.nix
index 4eb0fecec407..486172ac51f4 100644
--- a/pkgs/applications/editors/emacs/macport.nix
+++ b/pkgs/applications/editors/emacs/macport.nix
@@ -53,6 +53,10 @@ stdenv.mkDerivation rec {
 
     # use newer emacs icon
     cp nextstep/Cocoa/Emacs.base/Contents/Resources/Emacs.icns mac/Emacs.app/Contents/Resources/Emacs.icns
+
+    # Fix sandbox impurities.
+    substituteInPlace Makefile.in --replace '/bin/pwd' 'pwd'
+    substituteInPlace lib-src/Makefile.in --replace '/bin/pwd' 'pwd'
   '';
 
   configureFlags = [
diff --git a/pkgs/applications/editors/vscode/default.nix b/pkgs/applications/editors/vscode/default.nix
index 0c0441f20257..78d7d96d3961 100644
--- a/pkgs/applications/editors/vscode/default.nix
+++ b/pkgs/applications/editors/vscode/default.nix
@@ -18,16 +18,16 @@ let
   }.${system};
 
   sha256 = {
-    "i686-linux" = "09mgvff27iljj9z7h0xxmr6152hcxh7qqxl3i7wdc55ra1rsjq1n";
-    "x86_64-linux" = "1gvlvg3cjsscx6khy5gxd4wnb069kska00qdfwcq4kn7x1z04xnz";
-    "x86_64-darwin" = "1mf9nyjnxgmzai7rfd1rkwk0wvil0ripg3mh8icg4mld2jjz8rsy";
+    "i686-linux" = "04kbx1cx40lsy9irxy1arp1rixzk49ldhg34w3llmfbx63a4hchf";
+    "x86_64-linux" = "1plvx0mjcbizl6iffib95p5224r9frf0mn6c5xp14p3qnrp32jhm";
+    "x86_64-darwin" = "14h9gs6jpxydgd1h16ybq3ifw5jc7k83yg22pw3sk6vhy7hx7pxr";
   }.${system};
 
   archive_fmt = if system == "x86_64-darwin" then "zip" else "tar.gz";
 in
   stdenv.mkDerivation rec {
     name = "vscode-${version}";
-    version = "1.31.0";
+    version = "1.31.1";
 
     src = fetchurl {
       name = "VSCode_${version}_${plat}.${archive_fmt}";
@@ -126,7 +126,7 @@ in
         and code refactoring. It is also customizable, so users can change the
         editor's theme, keyboard shortcuts, and preferences
       '';
-      homepage = http://code.visualstudio.com/;
+      homepage = https://code.visualstudio.com/;
       downloadPage = https://code.visualstudio.com/Updates;
       license = licenses.unfree;
       maintainers = with maintainers; [ eadwu ];
diff --git a/pkgs/applications/misc/twmn/default.nix b/pkgs/applications/misc/twmn/default.nix
index 0667ec49b328..04c6cc3606e3 100644
--- a/pkgs/applications/misc/twmn/default.nix
+++ b/pkgs/applications/misc/twmn/default.nix
@@ -1,12 +1,13 @@
-{ stdenv, fetchgit, qtbase, qtx11extras, qmake, pkgconfig, boost }:
+{ stdenv, fetchFromGitHub, qtbase, qtx11extras, qmake, pkgconfig, boost }:
 
 stdenv.mkDerivation rec {
-  name = "twmn-git-2014-09-23";
+  name = "twmn-git-2018-10-01";
 
-  src = fetchgit {
-    url = "https://github.com/sboli/twmn.git";
-    rev = "9492a47e25547e602dd57efd807033677c90b150";
-    sha256 = "1a68gka9gyxyzhc9rn8df59rzcdwkjw90cxp1kk0rdfp6svhxhsa";
+  src = fetchFromGitHub {
+    owner = "sboli";
+    repo = "twmn";
+    rev = "80f48834ef1a07087505b82358308ee2374b6dfb";
+    sha256 = "0mpjvp800x07lp9i3hfcc5f4bqj1fj4w3dyr0zwaxc6wqmm0fdqz";
   };
 
   nativeBuildInputs = [ pkgconfig qmake ];
diff --git a/pkgs/applications/networking/remote/remmina/default.nix b/pkgs/applications/networking/remote/remmina/default.nix
index a53bea23e199..c2ae02e01491 100644
--- a/pkgs/applications/networking/remote/remmina/default.nix
+++ b/pkgs/applications/networking/remote/remmina/default.nix
@@ -13,13 +13,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "remmina";
-  version = "1.3.0";
+  version = "1.3.2";
 
   src = fetchFromGitLab {
     owner  = "Remmina";
     repo   = "Remmina";
     rev    = "v${version}";
-    sha256 = "15b0fnv7xra4fpmn2y4k2rpzcss30sd1dhnx7yvhs2zq12z2m0wi";
+    sha256 = "1ld5ik2g4b95z9pynmwx8mqhblbfzr7a0v35pms89ig4ck1kvr5r";
   };
 
   nativeBuildInputs = [ cmake ninja pkgconfig wrapGAppsHook ];
diff --git a/pkgs/applications/networking/soapui/default.nix b/pkgs/applications/networking/soapui/default.nix
index 93ab6c56d99d..1034acf0b90f 100644
--- a/pkgs/applications/networking/soapui/default.nix
+++ b/pkgs/applications/networking/soapui/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "soapui-${version}";
-  version = "5.4.0";
+  version = "5.5.0";
 
   src = fetchurl {
     url = "https://s3.amazonaws.com/downloads.eviware/soapuios/${version}/SoapUI-${version}-linux-bin.tar.gz";
-    sha256 = "1yqx1fsh8mr5zf36df7pi25dysb28gfscr1667jzd5s0k9jl42xd";
+    sha256 = "0v1wiy61jgvlxjk8qdvcnyn1gh2ysxf266zln7r4wpzwd5gc3dpw";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix
index 176d075f5fb3..57cecb3cb4cd 100644
--- a/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/pkgs/applications/science/astronomy/gildas/default.nix
@@ -7,8 +7,8 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "jan19b";
-  version = "20190101_b";
+  srcVersion = "feb19b";
+  version = "20190201_b";
   name = "gildas-${version}";
 
   src = fetchurl {
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     # source code of the previous release to a different directory
     urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz"
       "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz" ];
-    sha256 = "1wb4qj0j5n0k49zs5d7ndyzff8mapcb06i55jn0djzd023h0bwhp";
+    sha256 = "5b6da12ac869176d7a9a3d6a6620db1dbaa44a4785e2dd59dd1a8c38ea9cab87";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index e56c63e01bf0..4e8829f7e31c 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -17,6 +17,7 @@
 , cudnnSupport ? false, cudnn ? null
 , ncclSupport ? false, nccl ? null
 , pythonSupport ? false, python ? null, numpy ? null
+, substituteAll
 }:
 
 assert leveldbSupport -> (leveldb != null && snappy != null);
@@ -50,7 +51,9 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake doxygen ];
 
   cmakeFlags =
-    [ (if pythonSupport then "-Dpython_version=${python.version}" else "-DBUILD_python=OFF")
+    # It's important that caffe is passed the major and minor version only because that's what
+    # boost_python expects
+    [ (if pythonSupport then "-Dpython_version=3${python.pythonVersion}" else "-DBUILD_python=OFF")
       "-DBLAS=open"
     ] ++ (if cudaSupport then [
            "-DCUDA_ARCH_NAME=All"
@@ -75,16 +78,21 @@ stdenv.mkDerivation rec {
   outputs = [ "bin" "out"];
   propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
 
-  patches = [ ./darwin.patch ];
+  patches = [
+    ./darwin.patch
+  ] ++ lib.optional pythonSupport (substituteAll {
+    src = ./python.patch;
+    inherit (python.sourceVersion) major minor;  # Should be changed in case of PyPy
+  });
 
-  preConfigure = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
+  postPatch = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
     # CUDA 9.0 doesn't support sm_20
     sed -i 's,20 21(20) ,,' cmake/Cuda.cmake
-  '' + lib.optionalString (python.isPy3 or false) ''
-    sed -i \
-      -e 's,"python-py''${boost_py_version}",python3,g' \
-      -e 's,''${Boost_PYTHON-PY''${boost_py_version}_FOUND},''${Boost_PYTHON3_FOUND},g' \
-      cmake/Dependencies.cmake
+  '';
+
+  preConfigure = lib.optionalString pythonSupport ''
+    # We need this when building with Python bindings
+    export BOOST_LIBRARYDIR="${boost.out}/lib";
   '';
 
   postInstall = ''
diff --git a/pkgs/applications/science/math/caffe/python.patch b/pkgs/applications/science/math/caffe/python.patch
new file mode 100644
index 000000000000..b1bed6c174b8
--- /dev/null
+++ b/pkgs/applications/science/math/caffe/python.patch
@@ -0,0 +1,70 @@
+commit b14ca23651d390fcae4a929dedc7c33a83453a66
+Author: Frederik Rietdijk <fridh@fridh.nl>
+Date:   Sun Feb 17 08:41:27 2019 +0100
+
+    Find boost_pythonXX
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 08f56a33..0a04592a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -99,10 +99,10 @@ add_subdirectory(docs)
+ add_custom_target(lint COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/cmake/lint.cmake)
+ 
+ # ---[ pytest target
+-if(BUILD_python)
+-  add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
+-  add_dependencies(pytest pycaffe)
+-endif()
++# if(BUILD_python)
++#   add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
++#   add_dependencies(pytest pycaffe)
++# endif()
+ 
+ # ---[ uninstall target
+ configure_file(
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 4a5bac47..be026d43 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -141,37 +141,14 @@ if(BUILD_python)
+     # use python3
+     find_package(PythonInterp 3.0)
+     find_package(PythonLibs 3.0)
+-    find_package(NumPy 1.7.1)
+-    # Find the matching boost python implementation
+-    set(version ${PYTHONLIBS_VERSION_STRING})
+-
+-    STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-    find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-    set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-    while(NOT "${version}" STREQUAL "" AND NOT Boost_PYTHON_FOUND)
+-      STRING( REGEX REPLACE "([0-9.]+).[0-9]+" "\\1" version ${version} )
+-
+-      STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-      find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-      set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-      STRING( REGEX MATCHALL "([0-9.]+).[0-9]+" has_more_version ${version} )
+-      if("${has_more_version}" STREQUAL "")
+-        break()
+-      endif()
+-    endwhile()
+-    if(NOT Boost_PYTHON_FOUND)
+-      find_package(Boost 1.46 COMPONENTS python)
+-    endif()
+   else()
+     # disable Python 3 search
+     find_package(PythonInterp 2.7)
+     find_package(PythonLibs 2.7)
+-    find_package(NumPy 1.7.1)
+-    find_package(Boost 1.46 COMPONENTS python)
+   endif()
+-  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND)
++  find_package(NumPy 1.7.1)
++  find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@)
++  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND BOOST_PYTHON@major@@minor@_FOUND)
+     set(HAVE_PYTHON TRUE)
+     if(BUILD_python_layer)
+       list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER)
diff --git a/pkgs/applications/version-management/git-and-tools/git-cola/default.nix b/pkgs/applications/version-management/git-and-tools/git-cola/default.nix
index 039da03efb1f..3020e7d64aa8 100644
--- a/pkgs/applications/version-management/git-and-tools/git-cola/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/git-cola/default.nix
@@ -5,13 +5,13 @@ let
 
 in buildPythonApplication rec {
   name = "git-cola-${version}";
-  version = "3.2";
+  version = "3.3";
 
   src = fetchFromGitHub {
     owner = "git-cola";
     repo = "git-cola";
     rev = "v${version}";
-    sha256 = "1ivaqhvdbmlp0lmrwb2pv3kjqlcpqbxbinbvjjn3g81r4avjs7yy";
+    sha256 = "0gfbzcmaqg6hdy2cfpshgcwh8zgj1ia1vd95i5xdrsvksgb8fq2j";
   };
 
   buildInputs = [ git gettext ];
diff --git a/pkgs/applications/version-management/git-and-tools/hub/default.nix b/pkgs/applications/version-management/git-and-tools/hub/default.nix
index c6e62265b95b..8ae600ed3605 100644
--- a/pkgs/applications/version-management/git-and-tools/hub/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/hub/default.nix
@@ -1,25 +1,26 @@
-{ stdenv, buildGoPackage, fetchFromGitHub, ronn, ruby, groff, Security, utillinux }:
+{ stdenv, buildGoPackage, fetchFromGitHub, ronn, ruby, groff, Security, utillinux, git, glibcLocales }:
 
 buildGoPackage rec {
-  name = "hub-${version}";
-  version = "2.7.0";
+  pname = "hub";
+  version = "2.9.0";
 
   goPackagePath = "github.com/github/hub";
 
+  # Only needed to build the man-pages
+  excludedPackages = [ "github.com/github/hub/md2roff-bin" ];
+
   src = fetchFromGitHub {
     owner = "github";
-    repo = "hub";
+    repo = pname;
     rev = "v${version}";
-    sha256 = "1p90m1xp3jahs5y0lp0qfmfa7wqn7gxyygn7x45a6cbf2zzlb86l";
+    sha256 = "0yxpr606xx23l8823hjqj16cvjjrwb28c7z08ml1pkfvaf7w4n81";
   };
 
-  nativeBuildInputs = [ groff ronn utillinux ];
+  nativeBuildInputs = [ groff ronn utillinux glibcLocales ];
   buildInputs = [ ruby ] ++
     stdenv.lib.optional stdenv.isDarwin Security;
 
   postPatch = ''
-    mkdir bin
-    ln -s ${ronn}/bin/ronn bin/ronn
     patchShebangs .
   '';
 
@@ -29,13 +30,12 @@ buildGoPackage rec {
     install -D etc/hub.bash_completion.sh "$bin/share/bash-completion/completions/hub"
     install -D etc/hub.fish_completion  "$bin/share/fish/vendor_completions.d/hub.fish"
 
-    make man-pages
+    PATH=$PATH:${git}/bin LC_ALL=en_US.utf-8 make man-pages
     cp -vr --parents share/man/man[1-9]/*.[1-9] $bin/
   '';
 
   meta = with stdenv.lib; {
     description = "Command-line wrapper for git that makes you better at GitHub";
-
     license = licenses.mit;
     homepage = https://hub.github.com/;
     maintainers = with maintainers; [ the-kenny ];
diff --git a/pkgs/applications/virtualization/singularity/default.nix b/pkgs/applications/virtualization/singularity/default.nix
index 985f46ed9607..ab9416fd3d68 100644
--- a/pkgs/applications/virtualization/singularity/default.nix
+++ b/pkgs/applications/virtualization/singularity/default.nix
@@ -1,64 +1,77 @@
-{ stdenv
+{stdenv
+, removeReferencesTo
+, lib
+, fetchgit
 , fetchFromGitHub
-, autoreconfHook
-, gnutar
-, which
-, gnugrep
+, utillinux
+, openssl
 , coreutils
-, python
-, e2fsprogs
+, gawk
+, go
+, which
 , makeWrapper
 , squashfsTools
-, gzip
-, gnused
-, curl
-, utillinux
-, libarchive
-, file
- }:
+, buildGoPackage}:
+
+with lib;
 
-stdenv.mkDerivation rec {
+buildGoPackage rec {
   name = "singularity-${version}";
-  version = "2.6.1";
+  version = "3.0.1";
+
+  src = fetchFromGitHub {
+    owner = "sylabs";
+    repo = "singularity";
+    rev = "v${version}";
+    sha256 = "1wpsd0il2ipa2n5cnbj8dzs095jycdryq2rx62kikbq7ahzz4fsi";
+  };
+
+  goPackagePath = "github.com/sylabs/singularity";
+  goDeps = ./deps.nix;
 
-  enableParallelBuilding = true;
+  buildInputs = [ openssl ];
+  nativeBuildInputs = [ removeReferencesTo utillinux which makeWrapper ];
+  propagatedBuildInputs = [ coreutils squashfsTools ];
 
-  patches = [ ./env.patch ];
+  postConfigure = ''
+    find . -name vendor -type d -print0 | xargs -0 rm -rf
+
+    cd go/src/github.com/sylabs/singularity
 
-  preConfigure = ''
-    sed -i 's/-static//g' src/Makefile.am
     patchShebangs .
-    substituteInPlace libexec/bootstrap-scripts/deffile-sections.sh \
-      --replace /bin/cp ${coreutils}/bin/cp
+    sed -i 's|defaultEnv := "/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin"|defaultEnv := "${stdenv.lib.makeBinPath propagatedBuildInputs}"|' src/cmd/singularity/cli/singularity.go
+
+    ./mconfig -V ${version} -p $bin --localstatedir=/var
+    touch builddir/.dep-done
+    touch builddir/vendors-done
+
+    # Don't install SUID binaries
+    sed -i 's/-m 4755/-m 755/g' builddir/Makefile
+
+    # Point to base gopath
+    sed -i "s|^cni_vendor_GOPATH :=.*\$|cni_vendor_GOPATH := $NIX_BUILD_TOP/go/src/github.com/containernetworking/plugins/plugins|" builddir/Makefile
   '';
 
-  configureFlags = [ "--localstatedir=/var" ];
-  installFlags = "CONTAINER_MOUNTDIR=dummy CONTAINER_FINALDIR=dummy CONTAINER_OVERLAY=dummy SESSIONDIR=dummy";
-
-  fixupPhase = ''
-    patchShebangs $out
-    for f in $out/libexec/singularity/helpers/help.sh $out/libexec/singularity/cli/*.exec $out/libexec/singularity/bootstrap-scripts/*.sh ; do
-      chmod a+x $f
-      sed -i 's| /sbin/| |g' $f
-      sed -i 's| /bin/bash| ${stdenv.shell}|g' $f
-      wrapProgram $f --prefix PATH : ${stdenv.lib.makeBinPath buildInputs}
-    done
+  buildPhase = ''
+    make -C builddir
   '';
 
-  src = fetchFromGitHub {
-    owner = "singularityware";
-    repo = "singularity";
-    rev = version;
-    sha256 = "0q8qq9l3s6mv74km9h8gsn5mpd0m98dhmx8vph1jp6wnrr4xyfqf";
-  };
+  installPhase = ''
+    make -C builddir install LOCALSTATEDIR=$bin/var
+    chmod 755 $bin/libexec/singularity/bin/starter-suid
+  '';
 
-  nativeBuildInputs = [ autoreconfHook makeWrapper ];
-  buildInputs = [ coreutils gnugrep python e2fsprogs which gnutar squashfsTools gzip gnused curl utillinux libarchive file ];
+  postFixup = ''
+    find $bin/ -type f -executable -exec remove-references-to -t ${go} '{}' + || true
+
+    # These etc scripts shouldn't have their paths patched
+    cp etc/actions/* $bin/etc/singularity/actions/
+  '';
 
   meta = with stdenv.lib; {
-    homepage = http://singularity.lbl.gov/;
-    description = "Designed around the notion of extreme mobility of compute and reproducible science, Singularity enables users to have full control of their operating system environment";
-    license = "BSD license with 2 modifications";
+    homepage = http://www.sylabs.io/;
+    description = "Application containers for linux";
+    license = licenses.bsd3;
     platforms = platforms.linux;
     maintainers = [ maintainers.jbedo ];
   };
diff --git a/pkgs/applications/virtualization/singularity/deps.nix b/pkgs/applications/virtualization/singularity/deps.nix
new file mode 100644
index 000000000000..526202e75ae5
--- /dev/null
+++ b/pkgs/applications/virtualization/singularity/deps.nix
@@ -0,0 +1,669 @@
+# file generated from Gopkg.lock using dep2nix (https://github.com/nixcloud/dep2nix)
+[
+  {
+    goPackagePath  = "github.com/Microsoft/go-winio";
+    fetch = {
+      type = "git";
+      url = "https://github.com/Microsoft/go-winio";
+      rev =  "7da180ee92d8bd8bb8c37fc560e673e6557c392f";
+      sha256 = "19gjjhmzswhm11wzj38r5alxypmflmy0z42flhc3czhmmwv7b1av";
+    };
+  }
+  {
+    goPackagePath  = "github.com/alexflint/go-filemutex";
+    fetch = {
+      type = "git";
+      url = "https://github.com/alexflint/go-filemutex";
+      rev =  "d358565f3c3f5334209f1e80693e4f621650c489";
+      sha256 = "19fzbm0x8821awsmqj9ig49dxxkd72p1yfqbijmdwwszvw2r0ggz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/beorn7/perks";
+    fetch = {
+      type = "git";
+      url = "https://github.com/beorn7/perks";
+      rev =  "3a771d992973f24aa725d07868b467d1ddfceafb";
+      sha256 = "1l2lns4f5jabp61201sh88zf3b0q793w4zdgp9nll7mmfcxxjif3";
+    };
+  }
+  {
+    goPackagePath  = "github.com/blang/semver";
+    fetch = {
+      type = "git";
+      url = "https://github.com/blang/semver";
+      rev =  "2ee87856327ba09384cabd113bc6b5d174e9ec0f";
+      sha256 = "13ws259bwcibkclbr82ilhk6zadm63kxklxhk12wayklj8ghhsmy";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containerd/cgroups";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containerd/cgroups";
+      rev =  "5017d4e9a9cf2d4381db99eacd9baf84b95bfb14";
+      sha256 = "02pvcmj91j3maa9j1v91m2z9kpa6p822h06r007b3pl7h0paiqnj";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containerd/continuity";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containerd/continuity";
+      rev =  "246e49050efdf45e8f17fbbcf1547ee376f9939e";
+      sha256 = "1zc1f0yixf32lprp5r77z2j9xq7fk0hijq8xzl08j4zrk0fcy8aq";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containernetworking/cni";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containernetworking/cni";
+      rev =  "a7885cb6f8ab03fba07852ded351e4f5e7a112bf";
+      sha256 = "00ajs2r5r2z3l0vqwxrcwhjfc9px12qbcv5vnvs2mdipvvls1y2y";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containernetworking/plugins";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containernetworking/plugins";
+      rev =  "2b8b1ac0af4568e928d96ccc5f47b075416eeabd";
+      sha256 = "1yl9m8pwjmqxj3hf0w9s6rykszhcww54z07yjgxzabmqf2dhchxv";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containers/image";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containers/image";
+      rev =  "2e4f799f5eba49a2498d2793cfb2a4bc823ca3f6";
+      sha256 = "0b9symgbkd2vgvp7mfpz1l03i2zivwbc5ycccwv78b1ikk9m6b75";
+    };
+  }
+  {
+    goPackagePath  = "github.com/containers/storage";
+    fetch = {
+      type = "git";
+      url = "https://github.com/containers/storage";
+      rev =  "88d80428f9b146f8f9fe7e2e8cc8688a5aae1a4e";
+      sha256 = "13fagjisbg55dhgjd72h0hiy6jfg8ggkcnjl5haqj13c2gkf6sam";
+    };
+  }
+  {
+    goPackagePath  = "github.com/coreos/go-iptables";
+    fetch = {
+      type = "git";
+      url = "https://github.com/coreos/go-iptables";
+      rev =  "b5b1876b170881a8259f036445ee89c8669db386";
+      sha256 = "1s1c04x47pk3168606x4vkg4avs8a7m407hpha8py1xni08cgb6m";
+    };
+  }
+  {
+    goPackagePath  = "github.com/coreos/go-systemd";
+    fetch = {
+      type = "git";
+      url = "https://github.com/coreos/go-systemd";
+      rev =  "39ca1b05acc7ad1220e09f133283b8859a8b71ab";
+      sha256 = "1kzqrrzqspa5qm7kwslxl3m16lqzns23c24rv474ajzwmj3ixmx1";
+    };
+  }
+  {
+    goPackagePath  = "github.com/cpuguy83/go-md2man";
+    fetch = {
+      type = "git";
+      url = "https://github.com/cpuguy83/go-md2man";
+      rev =  "20f5889cbdc3c73dbd2862796665e7c465ade7d1";
+      sha256 = "1w22dfdamsq63b5rvalh9k2y7rbwfkkjs7vm9vd4a13h2ql70lg2";
+    };
+  }
+  {
+    goPackagePath  = "github.com/d2g/dhcp4";
+    fetch = {
+      type = "git";
+      url = "https://github.com/d2g/dhcp4";
+      rev =  "a1d1b6c41b1ce8a71a5121a9cee31809c4707d9c";
+      sha256 = "191hzw6yqzkm042h6miyycq3g0zrhqjhhpl27f8vhwzp4wanasiz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/d2g/dhcp4client";
+    fetch = {
+      type = "git";
+      url = "https://github.com/d2g/dhcp4client";
+      rev =  "e612998962035b93ba16cfd1ad2f3221985c1b8c";
+      sha256 = "1612wh99fblc9ashmm6mjc9110fhal95z0mn9qn7av3px13yd9fs";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/distribution";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/distribution";
+      rev =  "749f6afb4572201e3c37325d0ffedb6f32be8950";
+      sha256 = "05jn2wvikyw0pbmi74w5axr0zgxn5y3ynn9rhsq87rmwqj7raxhd";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/docker";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/docker";
+      rev =  "da99009bbb1165d1ac5688b5c81d2f589d418341";
+      sha256 = "02hhx7s8vm45rcl2mx9xamkncl2pb6qhsmz35mffbg4n6l5rn5x5";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/docker-credential-helpers";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/docker-credential-helpers";
+      rev =  "d68f9aeca33f5fd3f08eeae5e9d175edf4e731d1";
+      sha256 = "1ff829h5p1j6qiivjvnwyiybrff3dddv1ij71nz5whmgavdqgd49";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/go-connections";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/go-connections";
+      rev =  "3ede32e2033de7505e6500d6c868c2b9ed9f169d";
+      sha256 = "0v1pkr8apwmhyzbjfriwdrs1ihlk6pw7izm57r24mf9jdmg3fyb0";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/go-metrics";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/go-metrics";
+      rev =  "399ea8c73916000c64c2c76e8da00ca82f8387ab";
+      sha256 = "0najfy92fq05b330cnjk5b326yi7dnnmvzfk6g5lsa1fci78yzw4";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/go-units";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/go-units";
+      rev =  "47565b4f722fb6ceae66b95f853feed578a4a51c";
+      sha256 = "0npxsb3pp89slwf4a73fxm20hykad8xggij6i6hcd5jy19bjrd93";
+    };
+  }
+  {
+    goPackagePath  = "github.com/docker/libtrust";
+    fetch = {
+      type = "git";
+      url = "https://github.com/docker/libtrust";
+      rev =  "aabc10ec26b754e797f9028f4589c5b7bd90dc20";
+      sha256 = "1lwslbggzc2b0c4wxl5pn6i2nfgz5jz8f7s7vnid9mrlsk59h7s1";
+    };
+  }
+  {
+    goPackagePath  = "github.com/ghodss/yaml";
+    fetch = {
+      type = "git";
+      url = "https://github.com/ghodss/yaml";
+      rev =  "0ca9ea5df5451ffdf184b4428c902747c2c11cd7";
+      sha256 = "0skwmimpy7hlh7pva2slpcplnm912rp3igs98xnqmn859kwa5v8g";
+    };
+  }
+  {
+    goPackagePath  = "github.com/globalsign/mgo";
+    fetch = {
+      type = "git";
+      url = "https://github.com/globalsign/mgo";
+      rev =  "113d3961e7311526535a1ef7042196563d442761";
+      sha256 = "0m05ay993vv2jkc46bbdnq371s5jc0an2cycsj7p3b6lmv84jk9f";
+    };
+  }
+  {
+    goPackagePath  = "github.com/godbus/dbus";
+    fetch = {
+      type = "git";
+      url = "https://github.com/godbus/dbus";
+      rev =  "a389bdde4dd695d414e47b755e95e72b7826432c";
+      sha256 = "1ckvg15zdsgmbn4mi36cazkb407ixc9mmyf7vwj8b8wi3d00rgn9";
+    };
+  }
+  {
+    goPackagePath  = "github.com/gogo/protobuf";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gogo/protobuf";
+      rev =  "1adfc126b41513cc696b209667c8656ea7aac67c";
+      sha256 = "1j7azzlnihcvnd1apw5zr0bz30h7n0gyimqqkgc76vzb1n5dpi7m";
+    };
+  }
+  {
+    goPackagePath  = "github.com/golang/protobuf";
+    fetch = {
+      type = "git";
+      url = "https://github.com/golang/protobuf";
+      rev =  "b4deda0973fb4c70b50d226b1af49f3da59f5265";
+      sha256 = "0ya4ha7m20bw048m1159ppqzlvda4x0vdprlbk5sdgmy74h3xcdq";
+    };
+  }
+  {
+    goPackagePath  = "github.com/gorilla/context";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gorilla/context";
+      rev =  "08b5f424b9271eedf6f9f0ce86cb9396ed337a42";
+      sha256 = "03p4hn87vcmfih0p9w663qbx9lpsf7i7j3lc7yl7n84la3yz63m4";
+    };
+  }
+  {
+    goPackagePath  = "github.com/gorilla/mux";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gorilla/mux";
+      rev =  "e3702bed27f0d39777b0b37b664b6280e8ef8fbf";
+      sha256 = "0pvzm23hklxysspnz52mih6h1q74vfrdhjfm1l3sa9r8hhqmmld2";
+    };
+  }
+  {
+    goPackagePath  = "github.com/gorilla/websocket";
+    fetch = {
+      type = "git";
+      url = "https://github.com/gorilla/websocket";
+      rev =  "ea4d1f681babbce9545c9c5f3d5194a789c89f5b";
+      sha256 = "1bhgs2542qs49p1dafybqxfs2qc072xv41w5nswyrknwyjxxs2a1";
+    };
+  }
+  {
+    goPackagePath  = "github.com/hashicorp/errwrap";
+    fetch = {
+      type = "git";
+      url = "https://github.com/hashicorp/errwrap";
+      rev =  "7554cd9344cec97297fa6649b055a8c98c2a1e55";
+      sha256 = "0kmv0p605di6jc8i1778qzass18m0mv9ks9vxxrfsiwcp4la82jf";
+    };
+  }
+  {
+    goPackagePath  = "github.com/hashicorp/go-multierror";
+    fetch = {
+      type = "git";
+      url = "https://github.com/hashicorp/go-multierror";
+      rev =  "b7773ae218740a7be65057fc60b366a49b538a44";
+      sha256 = "09904bk7ac6qs9dgiv23rziq9h3makb9qg4jvxr71rlydsd7psfd";
+    };
+  }
+  {
+    goPackagePath  = "github.com/inconshreveable/mousetrap";
+    fetch = {
+      type = "git";
+      url = "https://github.com/inconshreveable/mousetrap";
+      rev =  "76626ae9c91c4f2a10f34cad8ce83ea42c93bb75";
+      sha256 = "1mn0kg48xkd74brf48qf5hzp0bc6g8cf5a77w895rl3qnlpfw152";
+    };
+  }
+  {
+    goPackagePath  = "github.com/j-keck/arping";
+    fetch = {
+      type = "git";
+      url = "https://github.com/j-keck/arping";
+      rev =  "2cf9dc699c5640a7e2c81403a44127bf28033600";
+      sha256 = "1bid8mpx3j4546ni0a6q5xyz7hb854g95qnxqmg5jzs9vrcird3c";
+    };
+  }
+  {
+    goPackagePath  = "github.com/kubernetes-sigs/cri-o";
+    fetch = {
+      type = "git";
+      url = "https://github.com/kubernetes-sigs/cri-o";
+      rev =  "8afc34092907d146906fcc31af112b2b46e7b5cd";
+      sha256 = "0ghcjvk7grdcwb1936mnj56a7rla804glfknid9kmr3kgny3yi43";
+    };
+  }
+  {
+    goPackagePath  = "github.com/magiconair/properties";
+    fetch = {
+      type = "git";
+      url = "https://github.com/magiconair/properties";
+      rev =  "c2353362d570a7bfa228149c62842019201cfb71";
+      sha256 = "1a10362wv8a8qwb818wygn2z48lgzch940hvpv81hv8gc747ajxn";
+    };
+  }
+  {
+    goPackagePath  = "github.com/mattn/go-runewidth";
+    fetch = {
+      type = "git";
+      url = "https://github.com/mattn/go-runewidth";
+      rev =  "9e777a8366cce605130a531d2cd6363d07ad7317";
+      sha256 = "0vkrfrz3fzn5n6ix4k8s0cg0b448459sldq8bp4riavsxm932jzb";
+    };
+  }
+  {
+    goPackagePath  = "github.com/mattn/go-shellwords";
+    fetch = {
+      type = "git";
+      url = "https://github.com/mattn/go-shellwords";
+      rev =  "02e3cf038dcea8290e44424da473dd12be796a8a";
+      sha256 = "1pg7pl25wvpl2dbpyrv9p1r7prnqimxlf6136vn0dfm54j2x4mnr";
+    };
+  }
+  {
+    goPackagePath  = "github.com/matttproud/golang_protobuf_extensions";
+    fetch = {
+      type = "git";
+      url = "https://github.com/matttproud/golang_protobuf_extensions";
+      rev =  "c12348ce28de40eed0136aa2b644d0ee0650e56c";
+      sha256 = "1d0c1isd2lk9pnfq2nk0aih356j30k3h1gi2w0ixsivi5csl7jya";
+    };
+  }
+  {
+    goPackagePath  = "github.com/mtrmac/gpgme";
+    fetch = {
+      type = "git";
+      url = "https://github.com/mtrmac/gpgme";
+      rev =  "b2432428689ca58c2b8e8dea9449d3295cf96fc9";
+      sha256 = "0hs9gfwf3cmnvmmxb485icwlv8h8xnny3p52bj7qwv251pvwsnaf";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/go-digest";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/go-digest";
+      rev =  "279bed98673dd5bef374d3b6e4b09e2af76183bf";
+      sha256 = "01gc7fpn8ax429024p2fcx3yb18axwz5bjf2hqxlii1jbsgw4bh9";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/image-spec";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/image-spec";
+      rev =  "e562b04403929d582d449ae5386ff79dd7961a11";
+      sha256 = "0j24nk975di8hcv6ycn2p2hhw1xdiy4bpxamr6wn12k21kadlp7s";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/image-tools";
+    fetch = {
+      type = "git";
+      url = "https://github.com/sylabs/image-tools";
+      rev =  "2814f498056809a9d5baaf76d1d82312180a5888";
+      sha256 = "0q3ljb51df5hc58rhp5xni2gsy3gkxn47d9dwyfcffnq8kpf9d8a";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/runc";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/runc";
+      rev =  "baf6536d6259209c3edfa2b22237af82942d3dfa";
+      sha256 = "09fm7f1k4lvx8v3crqb0cli1x2brlz8ka7f7qa8d2sb6ln58h7w7";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/runtime-spec";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/runtime-spec";
+      rev =  "5806c35637336642129d03657419829569abc5aa";
+      sha256 = "13vw1b3j9sx7d5fr3w3jdg137nnqcr50fqchq8z8nf6s18lkhj93";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/runtime-tools";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/runtime-tools";
+      rev =  "1c243a8a8eb44d491790798afc9b634c6f6a6380";
+      sha256 = "1ll5wrbn84yb2l7k6hpwwj06wywib7ar4z1bhh1rc5h9xajng7jq";
+    };
+  }
+  {
+    goPackagePath  = "github.com/opencontainers/selinux";
+    fetch = {
+      type = "git";
+      url = "https://github.com/opencontainers/selinux";
+      rev =  "ba1aefe8057f1d0cfb8e88d0ec1dc85925ef987d";
+      sha256 = "1n283j7rsim7gysm91x99c41d7vnsjsgfm4dy11fnzpkpzfiksq5";
+    };
+  }
+  {
+    goPackagePath  = "github.com/pelletier/go-toml";
+    fetch = {
+      type = "git";
+      url = "https://github.com/pelletier/go-toml";
+      rev =  "c01d1270ff3e442a8a57cddc1c92dc1138598194";
+      sha256 = "1fjzpcjng60mc3a4b2ql5a00d5gah84wj740dabv9kq67mpg8fxy";
+    };
+  }
+  {
+    goPackagePath  = "github.com/pkg/errors";
+    fetch = {
+      type = "git";
+      url = "https://github.com/pkg/errors";
+      rev =  "645ef00459ed84a119197bfb8d8205042c6df63d";
+      sha256 = "001i6n71ghp2l6kdl3qq1v2vmghcz3kicv9a5wgcihrzigm75pp5";
+    };
+  }
+  {
+    goPackagePath  = "github.com/pquerna/ffjson";
+    fetch = {
+      type = "git";
+      url = "https://github.com/pquerna/ffjson";
+      rev =  "d49c2bc1aa135aad0c6f4fc2056623ec78f5d5ac";
+      sha256 = "069w276lch2hhkvz26wdla8d4s0cg842bhqmih4sa33dsinlgs8g";
+    };
+  }
+  {
+    goPackagePath  = "github.com/prometheus/client_golang";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/client_golang";
+      rev =  "faf4ec335fe01ae5a6a0eaa34a5a9333bfbd1a30";
+      sha256 = "08xgqgx7vc27zc30chgi09lwrnvxr338dn624xnw4ysfm9r6lxrz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/prometheus/client_model";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/client_model";
+      rev =  "99fa1f4be8e564e8a6b613da7fa6f46c9edafc6c";
+      sha256 = "19y4ywsivhpxj7ikf2j0gm9k3cmyw37qcbfi78n526jxcc7kw998";
+    };
+  }
+  {
+    goPackagePath  = "github.com/prometheus/common";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/common";
+      rev =  "7600349dcfe1abd18d72d3a1770870d9800a7801";
+      sha256 = "0lsp94dqpj35dny4m4x15kg4wgwawlm3in7cnpajkkacgyxagk5f";
+    };
+  }
+  {
+    goPackagePath  = "github.com/prometheus/procfs";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/procfs";
+      rev =  "7d6f385de8bea29190f15ba9931442a0eaef9af7";
+      sha256 = "18cish8yas5r6xhgp8p8n7lg4wh3d4szzirszxra8m7rwy3swxxq";
+    };
+  }
+  {
+    goPackagePath  = "github.com/russross/blackfriday";
+    fetch = {
+      type = "git";
+      url = "https://github.com/russross/blackfriday";
+      rev =  "55d61fa8aa702f59229e6cff85793c22e580eaf5";
+      sha256 = "0qmavm5d14kj6im6sqzpqnlhpy524428vkn4hnfwknndr9rycmn0";
+    };
+  }
+  {
+    goPackagePath  = "github.com/safchain/ethtool";
+    fetch = {
+      type = "git";
+      url = "https://github.com/safchain/ethtool";
+      rev =  "6e3f4faa84e1d8d48afec75ed064cf3611d3f8bf";
+      sha256 = "15xjvny8bfhhjvvv654pimxxw5cd02q8skp1siwbfvrlw598j4lm";
+    };
+  }
+  {
+    goPackagePath  = "github.com/satori/go.uuid";
+    fetch = {
+      type = "git";
+      url = "https://github.com/satori/go.uuid";
+      rev =  "f58768cc1a7a7e77a3bd49e98cdd21419399b6a3";
+      sha256 = "1j4s5pfg2ldm35y8ls8jah4dya2grfnx2drb4jcbjsyrp4cm5yfb";
+    };
+  }
+  {
+    goPackagePath  = "github.com/seccomp/libseccomp-golang";
+    fetch = {
+      type = "git";
+      url = "https://github.com/seccomp/libseccomp-golang";
+      rev =  "e3496e3a417d1dc9ecdceca5af2513271fed37a0";
+      sha256 = "0z8v90nk22h8r5licav1a8cbn6k7bs47l0j1crw7bjl9hv1bmr71";
+    };
+  }
+  {
+    goPackagePath  = "github.com/sirupsen/logrus";
+    fetch = {
+      type = "git";
+      url = "https://github.com/sirupsen/logrus";
+      rev =  "c155da19408a8799da419ed3eeb0cb5db0ad5dbc";
+      sha256 = "0g5z7al7kky11ai2dhac6gkp3b5pxsvx72yj3xg4wg3265gbn7yz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/spf13/cobra";
+    fetch = {
+      type = "git";
+      url = "https://github.com/spf13/cobra";
+      rev =  "1e58aa3361fd650121dceeedc399e7189c05674a";
+      sha256 = "1d6dy60dw7i2mcab10yp99wi5w28jzhzzf16w4ys6bna7ymndiin";
+    };
+  }
+  {
+    goPackagePath  = "github.com/spf13/pflag";
+    fetch = {
+      type = "git";
+      url = "https://github.com/spf13/pflag";
+      rev =  "583c0c0531f06d5278b7d917446061adc344b5cd";
+      sha256 = "0nr4mdpfhhk94hq4ymn5b2sxc47b29p1akxd8b0hx4dvdybmipb5";
+    };
+  }
+  {
+    goPackagePath  = "github.com/sylabs/sif";
+    fetch = {
+      type = "git";
+      url = "https://github.com/sylabs/sif";
+      rev =  "177b9338f1ab9123be5b6217740be1f0ce924206";
+      sha256 = "1dwpml36n06hglp2km1wsfzdiw1yva6a0h00f1y2933m3i8r3k2w";
+    };
+  }
+  {
+    goPackagePath  = "github.com/syndtr/gocapability";
+    fetch = {
+      type = "git";
+      url = "https://github.com/syndtr/gocapability";
+      rev =  "33e07d32887e1e06b7c025f27ce52f62c7990bc0";
+      sha256 = "1x88c0b320b13w7samicf19dqx9rr4dnrh3yglk3cba21nwsp57i";
+    };
+  }
+  {
+    goPackagePath  = "github.com/vishvananda/netlink";
+    fetch = {
+      type = "git";
+      url = "https://github.com/vishvananda/netlink";
+      rev =  "a2ad57a690f3caf3015351d2d6e1c0b95c349752";
+      sha256 = "0hpzghf1a4cwawzhkiwdzin80h6hd09fskl77d5ppgc084yvj8x0";
+    };
+  }
+  {
+    goPackagePath  = "github.com/vishvananda/netns";
+    fetch = {
+      type = "git";
+      url = "https://github.com/vishvananda/netns";
+      rev =  "be1fbeda19366dea804f00efff2dd73a1642fdcc";
+      sha256 = "0j0xin37zp34ajmhsgfbxr8l7vrljf1lc6z3j3miidlmfwcl2s0m";
+    };
+  }
+  {
+    goPackagePath  = "github.com/xeipuuv/gojsonpointer";
+    fetch = {
+      type = "git";
+      url = "https://github.com/xeipuuv/gojsonpointer";
+      rev =  "4e3ac2762d5f479393488629ee9370b50873b3a6";
+      sha256 = "13y6iq2nzf9z4ls66bfgnnamj2m3438absmbpqry64bpwjfbsi9q";
+    };
+  }
+  {
+    goPackagePath  = "github.com/xeipuuv/gojsonreference";
+    fetch = {
+      type = "git";
+      url = "https://github.com/xeipuuv/gojsonreference";
+      rev =  "bd5ef7bd5415a7ac448318e64f11a24cd21e594b";
+      sha256 = "1xby79padc7bmyb8rfbad8wfnfdzpnh51b1n8c0kibch0kwc1db5";
+    };
+  }
+  {
+    goPackagePath  = "github.com/xeipuuv/gojsonschema";
+    fetch = {
+      type = "git";
+      url = "https://github.com/xeipuuv/gojsonschema";
+      rev =  "1d523034197ff1f222f6429836dd36a2457a1874";
+      sha256 = "1z8c6x8sfh6d1ib2lm2jps7r139qip6h3zik3fxhy1yr1380qbzp";
+    };
+  }
+  {
+    goPackagePath  = "go4.org";
+    fetch = {
+      type = "git";
+      url = "https://github.com/go4org/go4";
+      rev =  "9599cf28b011184741f249bd9f9330756b506cbc";
+      sha256 = "0hssb6jmpjxvdx2k1zx0l2dbwpx52zxcq5n2bhqivr670r4wdrkq";
+    };
+  }
+  {
+    goPackagePath  = "golang.org/x/crypto";
+    fetch = {
+      type = "git";
+      url = "https://github.com/sylabs/golang-x-crypto";
+      rev =  "4bce89e8e9a9f84a4cf02b9842c3eaff2af0a856";
+      sha256 = "11wi2zd055ym9m36ba007rdg4ghrwaiqxc77qyqc37ln7l7accr9";
+    };
+  }
+  {
+    goPackagePath  = "golang.org/x/net";
+    fetch = {
+      type = "git";
+      url = "https://go.googlesource.com/net";
+      rev =  "db08ff08e8622530d9ed3a0e8ac279f6d4c02196";
+      sha256 = "1f6q8kbijnrfy6wjqxrzgjf38ippckc5w34lhqsjs7kq045aar9a";
+    };
+  }
+  {
+    goPackagePath  = "golang.org/x/sys";
+    fetch = {
+      type = "git";
+      url = "https://go.googlesource.com/sys";
+      rev =  "6c888cc515d3ed83fc103cf1d84468aad274b0a7";
+      sha256 = "18anqrdajp4p015v3f5y641k3lmgp2jr0lfyx0pb3ia0qvn93mrp";
+    };
+  }
+  {
+    goPackagePath  = "gopkg.in/cheggaaa/pb.v1";
+    fetch = {
+      type = "git";
+      url = "https://github.com/cheggaaa/pb";
+      rev =  "2af8bbdea9e99e83b3ac400d8f6b6d1b8cbbf338";
+      sha256 = "0vxqiw6f3xyv0zy3g4lksf8za0z8i0hvfpw92hqimsy84f79j3dp";
+    };
+  }
+  {
+    goPackagePath  = "gopkg.in/yaml.v2";
+    fetch = {
+      type = "git";
+      url = "https://github.com/go-yaml/yaml";
+      rev =  "5420a8b6744d3b0345ab293f6fcba19c978f1183";
+      sha256 = "0dwjrs2lp2gdlscs7bsrmyc5yf6mm4fvgw71bzr9mv2qrd2q73s1";
+    };
+  }
+]
\ No newline at end of file
diff --git a/pkgs/applications/virtualization/singularity/env.patch b/pkgs/applications/virtualization/singularity/env.patch
deleted file mode 100644
index bc3be363bb81..000000000000
--- a/pkgs/applications/virtualization/singularity/env.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/libexec/functions b/libexec/functions
-index bc68107..6c2211c 100644
---- a/libexec/functions
-+++ b/libexec/functions
-@@ -29,16 +29,6 @@ if [ -z "${SINGULARITY_MESSAGELEVEL:-}" ]; then
-     SINGULARITY_MESSAGELEVEL=5
- fi
- 
--if [ -z "${USER:-}" ]; then
--    USER=`id -un`
--    export USER
--fi
--if [ -z "${HOME:-}" ]; then
--    HOME=`getent passwd "$USER" | cut -d : -f 6`
--    export HOME
--fi
--
--
- message() {
-     LEVEL="${1:-}"
-     MESSAGE="${2:-}"
diff --git a/pkgs/applications/window-managers/bspwm/default.nix b/pkgs/applications/window-managers/bspwm/default.nix
index dc57ad13d414..03652c749dee 100644
--- a/pkgs/applications/window-managers/bspwm/default.nix
+++ b/pkgs/applications/window-managers/bspwm/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   name = "bspwm-${version}";
-  version = "0.9.5";
+  version = "0.9.6";
 
   src = fetchFromGitHub {
     owner  = "baskerville";
     repo   = "bspwm";
     rev    = version;
-    sha256 = "09h3g1rxxjyw861mk32lj774nmwkx8cwxq4wfgmf4dpbizymvhhr";
+    sha256 = "1ywjhqxvggfdfd3cfki0vvlsli8lhqlziwfrj5vd57c6yisc2fyy";
   };
 
   buildInputs = [ libxcb libXinerama xcbutil xcbutilkeysyms xcbutilwm ];
diff --git a/pkgs/applications/window-managers/i3/status-rust.nix b/pkgs/applications/window-managers/i3/status-rust.nix
index 0e3168a5782d..178d111d79aa 100644
--- a/pkgs/applications/window-managers/i3/status-rust.nix
+++ b/pkgs/applications/window-managers/i3/status-rust.nix
@@ -1,21 +1,24 @@
-{ stdenv, rustPlatform, fetchFromGitHub, pkgconfig, dbus }:
+{ stdenv, rustPlatform, fetchFromGitHub, pkgconfig, dbus, libpulseaudio }:
 
 rustPlatform.buildRustPackage rec {
   name = "i3status-rust-${version}";
-  version = "0.9.0.2018-10-02";
+  version = "0.9.0.2019-02-15";
 
   src = fetchFromGitHub {
     owner = "greshake";
     repo = "i3status-rust";
-    rev = "11c2a21693ffcd0b6c2e0ac919b2232918293963";
-    sha256 = "019m9qpw7djq6g7lzbm7gjcavlgsp93g3cd7cb408nxnfsi7i9dp";
+    rev = "2dc958995834b529a245c22c510b57d5c928c747";
+    sha256 = "091a2pqgkiwnya2xv5rw5sj730hf6lvkp2kk5midsa3wz2dfbc2j";
   };
 
-  cargoSha256 = "1wnify730f7c3cb8wllqvs7pzrq54g5x81xspvz5gq0iqr0q38zc";
+  cargoSha256 = "06izzv86nkn1izapldysyryz9zvjxvq23c742z284bnxjfq5my6i";
 
   nativeBuildInputs = [ pkgconfig ];
 
-  buildInputs = [ dbus ];
+  buildInputs = [ dbus libpulseaudio ];
+
+  # Currently no tests are implemented, so we avoid building the package twice
+  doCheck = false;
 
   meta = with stdenv.lib; {
     description = "Very resource-friendly and feature-rich replacement for i3status";
diff --git a/pkgs/applications/window-managers/sway/beta.nix b/pkgs/applications/window-managers/sway/beta.nix
index 96e919df5a69..85a72e45de63 100644
--- a/pkgs/applications/window-managers/sway/beta.nix
+++ b/pkgs/applications/window-managers/sway/beta.nix
@@ -36,9 +36,9 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   mesonFlags = [
-    "-Dxwayland=enabled" "-Dgdk-pixbuf=enabled" "-Dman-pages=enabled"
+    "-Dxwayland=enabled" "-Dgdk-pixbuf=enabled"
     "-Dtray=enabled"
-  ];
+  ] ++ stdenv.lib.optional buildDocs "-Dman-pages=enabled";
 
   meta = with stdenv.lib; {
     description = "i3-compatible window manager for Wayland";