Merge commit '0c0954781e257b8b0dc49341795a2fe7d96945a3'

26 files changed, 434 insertions, 68 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
index eb7ba2a8c9c4..fb7963416167 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -6,13 +6,13 @@
 
 mkDerivation rec {
   name = "stellarium-${version}";
-  version = "0.18.3";
+  version = "0.19.0";
 
   src = fetchFromGitHub {
     owner = "Stellarium";
     repo = "stellarium";
     rev = "v${version}";
-    sha256 = "1cnwfk3vdsxh8gacw22qik401z0kpzd1ralbg9ph2cjqx9x2m1s1";
+    sha256 = "1x9s9v9ann93nyqd8n8adwhx66xgq5vp0liyzl1h1ji6qk8jla3c";
   };
 
   nativeBuildInputs = [ cmake perl ];
diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
index e97b5d1a3f4f..516608466a93 100644
--- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.3.4.3";
+  version = "2.3.5";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp";
+    sha256 = "12v240wnbc541hl4z2fiymxd3bd6czazs13fjkygldflg48w45m0";
   };
 
   buildInputs = [ zlib tbb python perl ];
diff --git a/nixpkgs/pkgs/applications/science/biology/itsx/default.nix b/nixpkgs/pkgs/applications/science/biology/itsx/default.nix
new file mode 100644
index 000000000000..804e71c1bfa7
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/itsx/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchurl, hmmer, perl }:
+
+stdenv.mkDerivation rec {
+  version = "1.1.1";
+  name = "itsx-${version}";
+
+  src = fetchurl {
+    url = "http://microbiology.se/sw/ITSx_${version}.tar.gz";
+    sha256 = "0lrmy2n3ax7f208k0k8l3yz0j5cpz05hv4hx1nnxzn0c51z1pc31";
+  };
+
+  buildInputs = [ hmmer perl ];
+
+  buildPhase = ''
+    sed -e "s,profileDB = .*,profileDB = \"$out/share/ITSx_db/HMMs\";," -i ITSx
+    sed "3 a \$ENV{\'PATH\'}='${hmmer}/bin:'.\"\$ENV{\'PATH\'}\";" -i ITSx
+    mkdir bin
+    mv ITSx bin
+  '';
+
+  installPhase = ''
+    mkdir -p $out/share/doc && cp -a bin $out/
+    cp *pdf $out/share/doc
+    cp -r ITSx_db $out/share
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing";
+    homepage = http://microbiology.se/software/itsx/;
+    license = licenses.gpl3;
+    maintainers = [ maintainers.bzizou ];
+    platforms = [ "x86_64-linux" "i686-linux" ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/megahit/default.nix b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix
new file mode 100644
index 000000000000..56bb35b64df8
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix
@@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub, zlib }:
+
+stdenv.mkDerivation rec {
+  pname    = "megahit";
+  version = "1.1.4";
+
+  src = fetchFromGitHub {
+    owner = "voutcn";
+    repo = "megahit";
+    rev = "v${version}";
+    sha256 = "011k0776w76l03zmy70kfd3y9zjmdnspfbs9fcxmnl3bdwd36kcw";
+  };
+
+  buildInputs = [ zlib ];
+
+  installPhase = ''
+    for bin in megahit_sdbg_build megahit megahit_asm_core megahit_toolkit; do
+        install -vD $bin $out/bin/$bin
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph";
+    license     = licenses.gpl3;
+    homepage    = https://github.com/voutcn/megahit;
+    maintainers = with maintainers; [ luispedro ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix
new file mode 100644
index 000000000000..dbbf8d39a93c
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix
@@ -0,0 +1,27 @@
+{ stdenv, fetchurl, cmake, gcc, gcc-unwrapped }:
+
+stdenv.mkDerivation rec {
+  version = "3.2.1"; 
+  name = "messer-slim-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/MesserLab/SLiM/archive/v${version}.tar.gz";
+    sha256 = "1j3ssjvxpsc21mmzj59kwimglz8pdazi5w6wplmx11x744k77wa1";
+  };
+
+  enableParallelBuilding = true;
+
+  nativeBuildInputs = [ cmake gcc gcc-unwrapped ];
+
+  cmakeFlags = [ "-DCMAKE_AR=${gcc-unwrapped}/bin/gcc-ar" 
+                 "-DCMAKE_RANLIB=${gcc-unwrapped}/bin/gcc-ranlib" ];
+
+  meta = {
+     description = "An evolutionary simulation framework";
+     homepage = https://messerlab.org/slim/;
+     license = with stdenv.lib.licenses; [ gpl3 ];
+     maintainers = with stdenv.lib.maintainers; [ bzizou ];
+     platforms = stdenv.lib.platforms.all;
+  };
+}
+
diff --git a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
index 3f28b5e31ccd..85c2b99b3a78 100644
--- a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix
@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "minimap2";
-  version = "2.15";
+  version = "2.16";
 
   src = fetchFromGitHub {
     repo = pname;
     owner = "lh3";
     rev = "v${version}";
-    sha256 = "0dy3m2wjmi3whjnmkj3maa1aadz525h7736wm8vvdcwq71ijqb7v";
+    sha256 = "1ggm5psv3gwsz627ik9kl6ry9gzgmfsvya6ni0gv6ahwlrhdim73";
   };
 
   buildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/biology/paml/default.nix b/nixpkgs/pkgs/applications/science/biology/paml/default.nix
index fe25a04c420a..68efc2030e53 100644
--- a/nixpkgs/pkgs/applications/science/biology/paml/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/paml/default.nix
@@ -1,11 +1,11 @@
 {stdenv, fetchurl}:
 
 stdenv.mkDerivation rec {
-  version = "4.9h";
+  version = "4.9i";
   name = "paml-${version}";
   src = fetchurl {
     url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz";
-    sha256 = "1czdfb3naadq0d3y42isrbyja33c3p28k8dv9mxlx2h19b7zcfv2";
+    sha256 = "1k5lcyls6c33ppp5fxl8ply2fy7i2k0gcqaifsl7gnc81d8ay4dw";
   };
 
   preBuild = ''
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
new file mode 100644
index 000000000000..01b1c0ba81bf
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
@@ -0,0 +1,19 @@
+{ stdenv, fetchurl, zlib }:
+    
+stdenv.mkDerivation rec {
+  pname = "stacks";
+  version = "2.3e";
+  src = fetchurl {
+    url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
+    sha256 = "046gmq8nzqy5v70ydqrhib2aiyrlja3cljvd37w4qbd4ryj3jr0w";
+  };
+
+  buildInputs = [ zlib ];
+
+  meta = {
+    description = "Software pipeline for building loci from short-read sequences";
+    homepage = http://catchenlab.life.illinois.edu/stacks/;
+    maintainers = [ stdenv.lib.maintainers.bzizou ];
+    license = stdenv.lib.licenses.gpl3;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index 7f5eb7b76e8c..c55766b8d615 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.29.31";
+  version = "14.29.32";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "15mxifm1h145bhyrm9rvmipvg048q8rgwg1sn6jmfgrimy0cjraj";
+    sha256 = "0jpl8smljyjpd3x1q6fcamgia1ij7gxk51faw99ys8ydnrzd57di";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix
index 99a8c777cd0e..35d21848e2b3 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/molden/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, which, gfortran, libGLU, xorg } :
 
 stdenv.mkDerivation rec {
-  version = "5.9.3";
+  version = "5.9.5";
   name = "molden-${version}";
 
   src = fetchurl {
     url = "ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden${version}.tar.gz";
-    sha256 = "18fz44g7zkm0xcx3w9hm049jv13af67ww7mb5b3kdhmza333a16q";
+    sha256 = "0va5g03kvnzydx0b77y1p536iy7swzvnx6yknp87qgpw1bgrzdj9";
   };
 
   nativeBuildInputs = [ which ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
index 2dd3c9b64c43..5fc71c9fc6ba 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  version = "8.3";
+  version = "8.4";
   fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; };
 
 in stdenv.mkDerivation {
@@ -11,7 +11,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz";
-    sha256 = "0nr3qmyfhp6fy8qrp4p43pl5xxfqgqg5g1c2775hxhpsi29xr7zf";
+    sha256 = "1fx5ssnf65b9ld7xs9rvvg8i80pblxpyhqkir0a7xshkk1g60z55";
   };
 
   nativeBuildInputs = [ perl procps fftw.dev ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix
index 7a7f1b3596d3..777b3499bedc 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix
@@ -4,12 +4,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "6.3";
+  version = "6.4";
   name = "quantum-espresso-${version}";
 
   src = fetchurl {
     url = "https://gitlab.com/QEF/q-e/-/archive/qe-${version}/q-e-qe-${version}.tar.gz";
-    sha256 = "1738z3nhkzcrgnhnfg1r4lipbwvcrcprwhzjbjysnylmzbzwhrs0";
+    sha256 = "1zjblzf0xzwmhmpjm56xvv8wsv5jmp5a204irzyicmd77p86c4vq";
   };
 
   passthru = {
@@ -20,12 +20,6 @@ stdenv.mkDerivation rec {
     patchShebangs configure
   '';
 
-  # remove after 6.3 version:
-  # makefile needs to ignore install directory easier than applying patch
-  preInstall = ''
-    printf "\n.PHONY: install\n" >> Makefile
-  '';
-
   buildInputs = [ fftw openblas gfortran ]
     ++ (stdenv.lib.optionals (mpi != null) [ mpi ]);
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
index b97ede413963..831ec9662b09 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -13,11 +13,11 @@ let
   in
   stdenv.mkDerivation rec {
     name = "eagle-${version}";
-    version = "9.1.2";
+    version = "9.3.1";
 
     src = fetchurl {
       url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz";
-      sha256 = "0y7ahl9z5a7l9cjk8hzmyv6ga8chlry5rr8v116q5mnsgs4i11an";
+      sha256 = "0hrbw368kskjzwjnqrri5j7c10d0z5m81h3s9zhqfrmwym42vdc5";
     };
 
     desktopItem = makeDesktopItem {
diff --git a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix
index d2246f656db0..e3c51906435e 100644
--- a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name    = "verilator-${version}";
-  version = "4.010";
+  version = "4.012";
 
   src = fetchurl {
     url    = "https://www.veripool.org/ftp/${name}.tgz";
-    sha256 = "0wfmazhxb6bf6qznh7v756fv7jayjgkzar33gazkwdwfwa7p8lan";
+    sha256 = "0xzndazp1g5qxzfirgiv219zmx7qyxfn7wsqbfq93cp1m6rp4pai";
   };
 
   enableParallelBuilding = true;
diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
index b5a6a5b963e5..eddc4b9b2080 100644
--- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
@@ -2,7 +2,7 @@
 
 rustPlatform.buildRustPackage rec {
   name = "elan-${version}";
-  version = "0.7.2";
+  version = "0.7.5";
 
   cargoSha256 = "0vv7kr7rc3lvas7ngp5dp99ajjd5v8k5937ish7zqz1k4970q2f1";
 
@@ -10,7 +10,7 @@ rustPlatform.buildRustPackage rec {
     owner = "kha";
     repo = "elan";
     rev = "v${version}";
-    sha256 = "0844fydfxvacyx02gwxbzpmiamsp22malyy5m4wpvrky4dkpn3qj";
+    sha256 = "1147f3lzr6lgvf580ppspn20bdwnf6l8idh1h5ana0p0lf5a0dn1";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/nixpkgs/pkgs/applications/science/logic/hol_light/default.nix b/nixpkgs/pkgs/applications/science/logic/hol_light/default.nix
index 099e2102c517..40b0115dc1b7 100644
--- a/nixpkgs/pkgs/applications/science/logic/hol_light/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/hol_light/default.nix
@@ -21,13 +21,13 @@ let
 in
 
 stdenv.mkDerivation {
-  name     = "hol_light-2018-09-30";
+  name     = "hol_light-2019-03-27";
 
   src = fetchFromGitHub {
     owner  = "jrh13";
     repo   = "hol-light";
-    rev    = "27e09dd27834de46e917057710e9d8ded51a4c9f";
-    sha256 = "1p0rm08wnc2lsrh3xzhlq3zdhzqcv1lbqnkwx3aybrqhbg1ixc1d";
+    rev    = "a2b487b38d9da47350f1b4316e34a8fa4cf7a40a";
+    sha256 = "1qlidl15qi8w4si8wxcmj8yg2srsb0q4k1ad9yd91sgx9h9aq8fk";
   };
 
   buildInputs = [ ocaml camlp5 ];
diff --git a/nixpkgs/pkgs/applications/science/math/ginac/default.nix b/nixpkgs/pkgs/applications/science/math/ginac/default.nix
index 18a5281bebb0..4b9f15e0a92f 100644
--- a/nixpkgs/pkgs/applications/science/math/ginac/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/ginac/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, cln, pkgconfig, readline, gmp, python }:
 
 stdenv.mkDerivation rec {
-  name = "ginac-1.7.4";
+  name = "ginac-1.7.5";
 
   src = fetchurl {
     url    = "${meta.homepage}/${name}.tar.bz2";
-    sha256 = "1vvqv73yk9klbq0mz239zzw77rlp72qcvzci4j1v6rafvji1616n";
+    sha256 = "11v8dpdfq8ybbbadyakp19xc7jgckplbbj6q2hh1c2hj5ps6njz7";
   };
 
   propagatedBuildInputs = [ cln ];
diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
index e3760533edae..8f96eb8f3060 100644
--- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg
 , zlib, libGLU_combined, libGLU, xorg }:
 
-let version = "4.2.1"; in
+let version = "4.2.2"; in
 
 stdenv.mkDerivation {
   name = "gmsh-${version}";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "1f11481e68900dc256f88aaed18d03e93b416ba01e9e8c3dc3f6d59a211f0561";
+    sha256 = "e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc";
   };
 
   buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined
diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix
index aef18abaedfb..beed2de9759c 100644
--- a/nixpkgs/pkgs/applications/science/math/nasc/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix
@@ -2,47 +2,45 @@
 , fetchFromGitHub
 , pkgconfig
 , gtk3
+, glib
 , pantheon
-, gnome3
+, libsoup
 , gtksourceview
 , libgee
 , cmake
 , libqalculate
-, gobject-introspection
-, wrapGAppsHook }:
+, cln
+, wrapGAppsHook
+}:
 
 stdenv.mkDerivation rec {
-  name = "nasc-${version}";
-  version = "0.5.1";
+  pname = "nasc";
+  version = "0.5.2";
 
   src = fetchFromGitHub {
     owner = "parnold-x";
-    repo = "nasc";
+    repo = pname;
     rev = version;
-    sha256 = "13y5fnm7g3xgdxmdydlgly73nigh8maqbf9d6c9bpyzxkxq1csy5";
+    sha256 = "009xmlsgl7r6wp6sczbdp8sjqqd6k2mychx5b4zn7wnrl7435y5y";
   };
 
-  postPatch = ''
-    # libqalculatenasc.so is not installed, and nasc fails to start
-    substituteInPlace libqalculatenasc/CMakeLists.txt --replace SHARED STATIC
-  '';
-
   nativeBuildInputs = [
     cmake
     pantheon.vala
-    gobject-introspection # for setup-hook
     pkgconfig
     wrapGAppsHook
   ];
 
   buildInputs = [
-    pantheon.elementary-icon-theme
+    cln
+    libsoup
+    gtk3
+    glib
     gtksourceview
     libgee
-    gnome3.libsoup
-    pantheon.granite
-    gtk3
     libqalculate
+    pantheon.elementary-icon-theme
+    pantheon.granite
   ];
 
   meta = with stdenv.lib; {
diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
index 5b431f419261..7351de53cfce 100644
--- a/nixpkgs/pkgs/applications/science/math/nauty/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
@@ -1,4 +1,8 @@
-{stdenv, fetchurl}:
+{ stdenv
+, lib
+, fetchurl
+, optimize ? false # impure
+}:
 stdenv.mkDerivation rec {
   name = "nauty-${version}";
   version = "26r11";
@@ -7,6 +11,13 @@ stdenv.mkDerivation rec {
     sha256 = "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y";
   };
   outputs = [ "out" "dev" ];
+  configureFlags = lib.optionals (!optimize) [
+    # Prevent nauty from sniffing some cpu features. While those are very
+    # widely available, it can lead to nasty bugs when they are not available:
+    # https://groups.google.com/forum/#!topic/sage-packaging/Pe4SRDNYlhA
+    "--disable-popcnt"
+    "--disable-clz"
+  ];
   buildInputs = [];
   installPhase = ''
     mkdir -p "$out"/{bin,share/doc/nauty} "$dev"/{lib,include/nauty}
@@ -14,18 +25,18 @@ stdenv.mkDerivation rec {
     find . -type f -perm -111 \! -name '*.*' \! -name configure -exec cp '{}' "$out/bin" \;
     cp [Rr][Ee][Aa][Dd]* COPYRIGHT This* [Cc]hange* "$out/share/doc/nauty"
 
-    cp *.h $dev/include/nauty
+    cp *.h "$dev/include/nauty"
     for i in *.a; do
       cp "$i" "$dev/lib/lib$i";
     done
   '';
   checkTarget = "checks";
-  meta = {
+  meta = with lib; {
     inherit version;
     description = ''Programs for computing automorphism groups of graphs and digraphs'';
-    license = stdenv.lib.licenses.asl20;
-    maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ raskin timokau ];
+    platforms = platforms.linux;
     homepage = http://pallini.di.uniroma1.it/;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 5104d1012b2f..61ebed896875 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, intltool, autoreconfHook, pkgconfig, libqalculate, gtk3, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
-  name = "qalculate-gtk-${version}";
-  version = "2.9.0";
+  pname = "qalculate-gtk";
+  version = "3.0.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "0c5s7mz8xwwmzc22yai8vqiww7paafkyi7khp8a2yws78m2nirdx";
+    sha256 = "00q6y9dgg9wgpgks79snbipn8alfjajlx02a5hm7wl9a20zd0b81";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index dd51059ff01b..75cd308da400 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -137,6 +137,13 @@ stdenv.mkDerivation rec {
 
     # https://trac.sagemath.org/ticket/27405
     ./patches/ignore-pip-deprecation.patch
+
+    # https://trac.sagemath.org/ticket/27360
+    (fetchpatch {
+      name = "eclib-20190226.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?id=f570e3a7fc2965764b84c04ce301a88ded2c42df";
+      sha256 = "0l5c4giixkn15v2a06sfzq5mkxila6l67zkjbacirwprrlpcnmmp";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
diff --git a/nixpkgs/pkgs/applications/science/misc/root/5.nix b/nixpkgs/pkgs/applications/science/misc/root/5.nix
index 1f0fc663647a..871f5ece9cfe 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/5.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/5.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cmake, pcre, pkgconfig, python2
+{ stdenv, fetchurl, fetchpatch, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lzma, gsl_1
 , Cocoa, OpenGL, cf-private, noSplash ? false }:
 
@@ -19,11 +19,30 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./sw_vers_root5.patch
+
+    (fetchpatch {
+      name = "enable_new_gcc.patch";
+      url = "https://aur.archlinux.org/cgit/aur.git/plain/enable_new_gcc.patch?h=root5&id=91c50876081a0af36f84ec4f0f9dba869107fa4f";
+      sha256 = "1rnp0xlw0yqi7mjs4w145njd79i8kkir1qik7zwicdik9axf8ygm";
+    })
+
+    # prevents rootcint from looking in /usr/includes and such
+    ./purify_include_paths_root5.patch
+
+    # disable dictionary generation for stuff that includes libc headers
+    # our glibc requires a modern compiler
+    ./disable_libc_dicts_root5.patch
   ];
 
   preConfigure = ''
     patchShebangs build/unix/
     ln -s ${stdenv.lib.getDev stdenv.cc.libc}/include/AvailabilityMacros.h cint/cint/include/
+  ''
+  # Fix CINTSYSDIR for "build" version of rootcint
+  # This is probably a bug that breaks out-of-source builds
+  + ''
+    substituteInPlace cint/cint/src/loadfile.cxx\
+      --replace 'env = "cint";' 'env = "'`pwd`'/cint";'
   '' + stdenv.lib.optionalString noSplash ''
     substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true"
   '';
@@ -73,8 +92,5 @@ stdenv.mkDerivation rec {
     description = "A data analysis framework";
     platforms = platforms.unix;
     maintainers = with maintainers; [ veprbl ];
-    # needs to be adapted to work with modern glibc
-    # it works on darwin by impurely picking up system's libc headers
-    broken = stdenv.isLinux;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch b/nixpkgs/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
new file mode 100644
index 000000000000..abd6222847ef
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/misc/root/disable_libc_dicts_root5.patch
@@ -0,0 +1,27 @@
+diff --git a/cint/ROOT/CMakeLists.txt b/cint/ROOT/CMakeLists.txt
+--- a/cint/ROOT/CMakeLists.txt
++++ b/cint/ROOT/CMakeLists.txt
+@@ -47,21 +47,13 @@ set(CINTSTLDLLHEADERS
+     ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+   )
+ set(CINTINCDLLNAMES 
+-    stdfunc 
++#    stdfunc 
+ #    stdcxxfunc
+    )
+ set(CINTINCDLLHEADERS
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
++#    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdfunc.h 
+ #    ${CMAKE_SOURCE_DIR}/cint/cint/lib/stdstrct/stdcxxfunc.h
+    )
+-if(NOT WIN32)
+-  set(CINTSTLDLLNAMES ${CINTSTLDLLNAMES}  valarray)
+-  set(CINTSTLDLLHEADERS ${CINTSTLDLLHEADERS} ${CINTDLLDIR}/vary.h)
+-  set(CINTINCDLLNAMES ${CINTINCDLLNAMES} posix ipc)
+-  set(CINTINCDLLHEADERS ${CINTINCDLLHEADERS} 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/posix/exten.h 
+-    ${CMAKE_SOURCE_DIR}/cint/cint/lib/ipc/ipcif.h)
+-endif()
+ 
+ set(CINTBUILDLOADER
+     vector 
diff --git a/nixpkgs/pkgs/applications/science/misc/root/purify_include_paths_root5.patch b/nixpkgs/pkgs/applications/science/misc/root/purify_include_paths_root5.patch
new file mode 100644
index 000000000000..6773603b8ad3
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/misc/root/purify_include_paths_root5.patch
@@ -0,0 +1,204 @@
+diff --git a/cint/cint/src/loadfile.cxx b/cint/cint/src/loadfile.cxx
+--- a/cint/cint/src/loadfile.cxx
++++ b/cint/cint/src/loadfile.cxx
+@@ -1365,92 +1365,6 @@ int G__statfilename(const char *filenamein, struct stat *statBuf,
+          }
+       }         
+ #endif /* G__EDU_VERSION */
+-      
+-#ifdef G__VISUAL
+-      /**********************************************
+-       * try /msdev/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/msdev/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif /* G__VISUAL */
+-         
+-#ifdef G__SYMANTEC
+-      /**********************************************
+-       * try /sc/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/sc/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif // G__SYMANTEC
+-         
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif
+-      
+-#ifdef __GNUC__
+-      /**********************************************
+-       * try /usr/include/g++/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/g++/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif /* __GNUC__ */
+-      
+-#ifndef G__WIN32
+-      /* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/CC/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/CC/%s%s",filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }         
+-#endif
+-         
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/codelibs/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         workname.Format("/usr/include/codelibs/%s%s"
+-                         ,filename(),addpost[i2]);
+-         res = stat( workname, statBuf );         
+-         if (res==0) {
+-            if (fullPath) fullPath->Swap(workname);
+-            return res;
+-         }
+-      }
+-#endif
+    }
+    return -1;
+ }
+@@ -1960,107 +1874,6 @@ int G__loadfile(const char *filenamein)
+       }
+       if(G__ifile.fp) break;
+ #endif /* G__EDU_VERSION */
+-
+-#ifdef G__VISUAL
+-      /**********************************************
+-       * try /msdev/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/msdev/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* G__VISUAL */
+-
+-#ifdef G__SYMANTEC
+-      /**********************************************
+-       * try /sc/include
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/sc/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* G__SYMANTEC */
+-
+-#ifndef G__WIN32
+-      /**********************************************
+-       * try /usr/include/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif
+-
+-#ifdef __GNUC__
+-      /**********************************************
+-       * try /usr/include/g++/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/g++/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-#endif /* __GNUC__ */
+-
+-#ifndef G__WIN32
+-/* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/CC/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-         G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/CC/%s%s",filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-/* #endif __hpux */
+-#endif
+-
+-#ifndef G__WIN32
+-/* #ifdef __hpux */
+-      /**********************************************
+-       * try /usr/include/codelibs/filename
+-       **********************************************/
+-      if('\0'!=G__cintsysdir[0]) {
+-        G__snprintf(G__ifile.name,G__MAXFILENAME,"/usr/include/codelibs/%s%s"
+-                    ,filename(),addpost[i2]);
+-#ifndef G__WIN32
+-        G__ifile.fp = fopen(G__ifile.name,"r");
+-#else
+-        G__ifile.fp = fopen(G__ifile.name,"rb");
+-#endif
+-        G__globalcomp=G__store_globalcomp;
+-      }
+-      if(G__ifile.fp) break;
+-/* #endif __hpux */
+-#endif
+     }
+   }
+ 
diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index a682d59ab23a..f0ac310ea665 100644
--- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -8,11 +8,11 @@
 
 
 stdenv.mkDerivation {
-  name = "gromacs-2019";
+  name = "gromacs-2019.1";
 
   src = fetchurl {
-    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.tar.gz";
-    sha256 = "02qd27pgc5kwkk68m8hwarkbb1b9z5rdrm67yjqyxd5my2jq3cn5";
+    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.1.tar.gz";
+    sha256 = "1v438nf6viwpl53ydrljf598cf8lh7jqxp5bzi74rrnhzk97xhxj";
   };
 
   buildInputs = [cmake fftw]