Merge master into staging-next

19 files changed, 164 insertions, 122 deletions

diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix
index 8552aa34c43..e43d48db55f 100644
--- a/pkgs/applications/science/biology/hmmer/default.nix
+++ b/pkgs/applications/science/biology/hmmer/default.nix
@@ -1,28 +1,25 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  version = "3.1b2";
+  version = "3.2.1";
   name = "hmmer-${version}";
 
   src = fetchurl {
-    url = "http://eddylab.org/software/hmmer3/${version}/${name}.tar.gz";
-    sha256 = "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx";
+    url = "http://eddylab.org/software/hmmer/${name}.tar.gz";
+    sha256 = "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5";
   };
 
   meta = with stdenv.lib; {
     description = "Biosequence analysis using profile hidden Markov models";
     longDescription = ''
-HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
-
-HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.
-
-HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
-
-HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute.
+      HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
+      HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.
+      HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
+      HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute.
     '';
     homepage = http://hmmer.org/;
     license = licenses.gpl3;
     maintainers = [ maintainers.iimog ];
-    platforms = platforms.linux;
+    platforms = [ "x86_64-linux" "i686-linux" ];
   };
 }
diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix
new file mode 100644
index 00000000000..9f24046b3bf
--- /dev/null
+++ b/pkgs/applications/science/biology/niftyreg/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, lib, fetchurl, cmake, zlib }:
+
+stdenv.mkDerivation rec {
+  pname   = "niftyreg";
+  version = "1.3.9";
+  name    = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/${pname}/nifty_reg-${version}/nifty_reg-${version}.tar.gz";
+    sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib ];
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg;
+    description = "Medical image registration software";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = [ "x86_64-linux" ];
+    license   = licenses.bsd3;
+  };
+}
diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix
new file mode 100644
index 00000000000..671ee4b95c6
--- /dev/null
+++ b/pkgs/applications/science/biology/niftyseg/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, lib, fetchurl, cmake, eigen, zlib }:
+
+stdenv.mkDerivation rec {
+  pname   = "niftyseg";
+  version = "1.0";
+  name = "${pname}-${version}";
+  src = fetchurl {
+    url    = "https://github.com/KCL-BMEIS/NiftySeg/archive/v${version}.tar.gz";
+    sha256 = "11q6yldsxp3k6gfp94c0xhcan2y3finzv8lzizmrc79yps3wjkn0";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ eigen zlib ];
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = http://cmictig.cs.ucl.ac.uk/research/software/software-nifty/niftyseg;
+    description = "Software for medical image segmentation, bias field correction, and cortical thickness calculation";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license   = licenses.bsd3;
+  };
+
+}
diff --git a/pkgs/applications/science/logic/coq2html/default.nix b/pkgs/applications/science/logic/coq2html/default.nix
index a987bf1ba57..d76462ca938 100644
--- a/pkgs/applications/science/logic/coq2html/default.nix
+++ b/pkgs/applications/science/logic/coq2html/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, make, fetchgit, ocaml }:
+{ stdenv, fetchgit, ocaml }:
 
 let 
   version = "20170720";
@@ -13,7 +13,7 @@ stdenv.mkDerivation {
     sha256 = "1x466j0pyjggyz0870pdllv9f5vpnfrgkd0w7ajvm9rkwyp3f610";
   };
 
-  buildInputs = [ make ocaml ];
+  buildInputs = [ ocaml ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/science/logic/tptp/default.nix b/pkgs/applications/science/logic/tptp/default.nix
index f3c4f22eae3..24971b500d3 100644
--- a/pkgs/applications/science/logic/tptp/default.nix
+++ b/pkgs/applications/science/logic/tptp/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   name = "TPTP-${version}";
-  version = "7.1.0";
+  version = "7.2.0";
 
   src = fetchurl {
-    url = [
+    urls = [
       "http://www.cs.miami.edu/~tptp/TPTP/Distribution/TPTP-v${version}.tgz"
       "http://www.cs.miami.edu/~tptp/TPTP/Archive/TPTP-v${version}.tgz"
     ];
-    sha256 = "0slqbqv4y43wz6wnh72s4n540ssapah0d12mndi0c7xr04kf2v2d";
+    sha256 = "0yq8452b6mym4yscy46pshg0z2my8xi74b5bp2qlxd5bjwcrg6rl";
   };
 
   nativeBuildInputs = [ patchelf ];
diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix
index f7d67d82cbc..29fc94a71da 100644
--- a/pkgs/applications/science/logic/z3/default.nix
+++ b/pkgs/applications/science/logic/z3/default.nix
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
     description = "A high-performance theorem prover and SMT solver";
     homepage    = "https://github.com/Z3Prover/z3";
     license     = stdenv.lib.licenses.mit;
-    platforms   = stdenv.lib.platforms.unix;
+    platforms   = stdenv.lib.platforms.x86_64;
     maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
   };
 }
diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix
index 0ac40b1e7d4..8de78092bd8 100644
--- a/pkgs/applications/science/machine-learning/shogun/default.nix
+++ b/pkgs/applications/science/machine-learning/shogun/default.nix
@@ -2,9 +2,9 @@
 # data, compression
 , bzip2, curl, hdf5, json_c, lzma, lzo, protobuf, snappy
 # maths
-, blas, eigen, nlopt, lp_solve, colpack
+, openblasCompat, eigen, nlopt, lp_solve, colpack
 # libraries
-, libarchive, liblapack, libxml2
+, libarchive, libxml2
 # extra support
 , pythonSupport ? true, pythonPackages ? null
 , opencvSupport ? false, opencv ? null
@@ -41,8 +41,8 @@ stdenv.mkDerivation rec {
   CCACHE_DIR=".ccache";
 
   buildInputs = with lib; [
-      blas bzip2 ccache cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
-      protobuf nlopt snappy swig (libarchive.dev) liblapack libxml2
+      openblasCompat bzip2 ccache cmake colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
+      protobuf nlopt snappy swig (libarchive.dev) libxml2
     ]
     ++ optionals (pythonSupport) (with pythonPackages; [ python ply numpy ])
     ++ optional  (opencvSupport) opencv;
diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix
index e62df7f11cc..94e0a44226d 100644
--- a/pkgs/applications/science/math/colpack/default.nix
+++ b/pkgs/applications/science/math/colpack/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation rec {
     vertex coloring and derivative computation";
     homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities";
     license = licenses.lgpl3;
+    platforms = platforms.linux;
     maintainers = with maintainers; [ edwtjo ];
   };
 
diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix
index 6a0b686602f..2823165d022 100644
--- a/pkgs/applications/science/math/giac/default.nix
+++ b/pkgs/applications/science/math/giac/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapackWithoutAtlas
+{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapack
 , gmp, mpfr, pari, ntl, gsl, blas, mpfi
 , readline, gettext, libpng, libao, gfortran, perl
 , enableGUI ? false, libGLU_combined ? null, xorg ? null, fltk ? null
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
     # gfortran.cc default output contains static libraries compiled without -fPIC
     # we want libgfortran.so.3 instead
     (stdenv.lib.getLib gfortran.cc)
-    liblapackWithoutAtlas
+    liblapack
   ] ++ stdenv.lib.optionals enableGUI [
     libGLU_combined fltk xorg.libX11
   ];
diff --git a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch b/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch
deleted file mode 100644
index 0326a8d296a..00000000000
--- a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -324,25 +324,16 @@
-         set_config_option(HAVE_BLAS "Blas(IntelMKL)")
-         set_config_option(HAVE_LAPACK "Lapack(IntelMKL)")
-       else(LAPACK_LIBRARIES)
--        # on Linux also try to find ATLAS without a Fortran compiler, because
--        # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx
--        set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas)
--        find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "")
-+        # try with generic names
-+        set(GENERIC_LIBS_REQUIRED lapack blas pthread)
-+        find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "")
-         if(LAPACK_LIBRARIES)
--          set_config_option(HAVE_BLAS "Blas(ATLAS)")
--          set_config_option(HAVE_LAPACK "Lapack(ATLAS)")
--        else(LAPACK_LIBRARIES)
--          # try with generic names
--          set(GENERIC_LIBS_REQUIRED lapack blas pthread)
--          find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "")
--          if(LAPACK_LIBRARIES)
--            set_config_option(HAVE_BLAS "Blas(Generic)")
--            set_config_option(HAVE_LAPACK "Lapack(Generic)")
--            find_library(GFORTRAN_LIB gfortran)
--            if(GFORTRAN_LIB)
--              list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB})
--            endif(GFORTRAN_LIB)
--          endif(LAPACK_LIBRARIES)
-+          set_config_option(HAVE_BLAS "Blas(Generic)")
-+          set_config_option(HAVE_LAPACK "Lapack(Generic)")
-+          find_library(GFORTRAN_LIB gfortran)
-+          if(GFORTRAN_LIB)
-+            list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB})
-+          endif(GFORTRAN_LIB)
-         endif(LAPACK_LIBRARIES)
-       endif(LAPACK_LIBRARIES)
-     elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS")
diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix
index 525fc5f1dc2..7c8e62cc97c 100644
--- a/pkgs/applications/science/math/gmsh/default.nix
+++ b/pkgs/applications/science/math/gmsh/default.nix
@@ -1,21 +1,17 @@
-{ stdenv, fetchurl, cmake, blas, liblapack, gfortran, gmm, fltk, libjpeg
+{ stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg
 , zlib, libGLU_combined, libGLU, xorg }:
 
-let version = "4.0.2"; in
+let version = "4.0.4"; in
 
 stdenv.mkDerivation {
   name = "gmsh-${version}";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "03aw3sbz4x998rk29az7mgm0mrdb6614aqnppg81p5jkh5097jgk";
+    sha256 = "1hvrls3xyxvn69kwicpvndrs0zhifcfkhfsxr8zkmhmn6fhnjhha";
   };
 
-  # The original CMakeLists tries to use some version of the Lapack lib
-  # that is supposed to work without Fortran but didn't for me.
-  patches = [ ./CMakeLists.txt.patch ];
-
-  buildInputs = [ cmake blas liblapack gmm fltk libjpeg zlib libGLU_combined
+  buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined
     libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext
     xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE
   ];
@@ -27,7 +23,7 @@ stdenv.mkDerivation {
   meta = {
     description = "A three-dimensional finite element mesh generator";
     homepage = http://gmsh.info/;
-    platforms = stdenv.lib.platforms.all;
+    platforms = [ "x86_64-linux" ];
     license = stdenv.lib.licenses.gpl2Plus;
   };
 }
diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix
index 06d448f6252..d4a4133d06e 100644
--- a/pkgs/applications/science/math/gurobi/default.nix
+++ b/pkgs/applications/science/math/gurobi/default.nix
@@ -33,9 +33,15 @@ stdenv.mkDerivation rec {
     cp include/gurobi*.h $out/include/
 
     mkdir -p $out/lib
+    cp lib/*.jar $out/lib/
+    cp lib/libGurobiJni*.so $out/lib/
     cp lib/libgurobi*.so* $out/lib/
     cp lib/libgurobi*.a $out/lib/
     cp src/build/*.a $out/lib/
+
+    mkdir -p $out/share/java
+    ln -s $out/lib/gurobi.jar $out/share/java/
+    ln -s $out/lib/gurobi-javadoc.jar $out/share/java/
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/math/pari/gp2c.nix b/pkgs/applications/science/math/pari/gp2c.nix
index 42f35edb256..4915e42025b 100644
--- a/pkgs/applications/science/math/pari/gp2c.nix
+++ b/pkgs/applications/science/math/pari/gp2c.nix
@@ -4,11 +4,11 @@
 stdenv.mkDerivation rec {
 
   name = "gp2c-${version}";
-  version = "0.0.11";
+  version = "0.0.11pl1";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${name}.tar.gz";
-    sha256 = "1z69xj2dpd8yyi8108rz26c50xpv0k2j8qnk0bzy1c5lw3pd1adm";
+    sha256 = "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s";
   };
 
   buildInputs = [ pari perl ];
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 7e62f0cf75e..cf8515283cd 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages_8_x;
+  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
 
   # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
   python = nixpkgs.python2.override {
@@ -26,7 +26,7 @@ let
       };
 
       sagenb = self.callPackage ./sagenb.nix {
-        mathjax = nodePackages_8_x.mathjax;
+        mathjax = nodePackages.mathjax;
       };
 
       sagedoc = self.callPackage ./sagedoc.nix {
@@ -36,8 +36,8 @@ let
       env-locations = self.callPackage ./env-locations.nix {
         inherit pari_data ecl;
         inherit singular;
-        three = nodePackages_8_x.three;
-        mathjax = nodePackages_8_x.mathjax;
+        three = nodePackages.three;
+        mathjax = nodePackages.mathjax;
       };
 
       sage-env = self.callPackage ./sage-env.nix {
@@ -49,7 +49,7 @@ let
         inherit pythonEnv;
         inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
-        three = nodePackages_8_x.three;
+        three = nodePackages.three;
       };
 
       sage = self.callPackage ./sage.nix { };
diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix
index 01bd1c6fd80..3571d705e31 100644
--- a/pkgs/applications/science/misc/boinc/default.nix
+++ b/pkgs/applications/science/misc/boinc/default.nix
@@ -1,10 +1,10 @@
 { fetchFromGitHub, stdenv, autoconf, automake, pkgconfig, m4, curl,
-libGLU_combined, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK, xcbutil,
+libGLU_combined, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK30, xcbutil,
 sqlite, gtk2, patchelf, libXScrnSaver, libnotify, libX11, libxcb }:
 
 let
-  majorVersion = "7.8";
-  minorVersion = "0";
+  majorVersion = "7.14";
+  minorVersion = "2";
 in
 
 stdenv.mkDerivation rec {
@@ -16,13 +16,13 @@ stdenv.mkDerivation rec {
     owner = "BOINC";
     repo = "boinc";
     rev = "client_release/${majorVersion}/${version}";
-    sha256 = "08kv3fai79cc28vmyi0y4xcdd5h9xgkn9yyc6y36c0mglaxsn4pr";
+    sha256 = "0nicpkag18xq0libfqqvs0im22mijpsxzfk272iwdd9l0lmgfvyd";
   };
 
   nativeBuildInputs = [ libtool automake autoconf m4 pkgconfig ];
 
   buildInputs = [
-    curl libGLU_combined libXmu libXi freeglut libjpeg wxGTK sqlite gtk2 libXScrnSaver
+    curl libGLU_combined libXmu libXi freeglut libjpeg wxGTK30 sqlite gtk2 libXScrnSaver
     libnotify patchelf libX11 libxcb xcbutil
   ];
 
diff --git a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix
new file mode 100644
index 00000000000..1986f3b75ec
--- /dev/null
+++ b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchurl
+, gfortran, mpi
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.10";
+  name = "DL_POLY_Classic-${version}";
+
+  src = fetchurl {
+    url = "https://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/574/8924/dl_class_1.10.tar.gz";
+    sha256 = "1r76zvln3bwycxlmqday0sqzv5j260y7mdh66as2aqny6jzd5ld7";
+  };
+
+  buildInputs = [ mpi gfortran ];
+
+  configurePhase = ''
+    cd source
+    cp -v ../build/MakePAR Makefile
+  '';
+
+  buildPhase = ''
+    make dlpoly
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -v ../execute/DLPOLY.X $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://www.ccp5.ac.uk/DL_POLY_C;
+    description = "DL_POLY Classic is a general purpose molecular dynamics simulation package";
+    license = licenses.bsdOriginal;
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ maintainers.costrouc ];
+  };
+}
diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
index 03e37ad9d93..f4491053e4c 100644
--- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
@@ -1,63 +1,56 @@
-{ lib
-, bash
-, stdenv
-, writeText
-, fetchFromGitHub
-, libpng
-, gzip
-, fftw
-, openblas
-, mpiSupport ? false, mpi ? null
+{ stdenv, fetchFromGitHub
+, libpng, gzip, fftw, openblas
+, mpi ? null
 }:
-
-assert mpiSupport -> mpi != null;
-
+let packages = [
+     "asphere" "body" "class2" "colloid" "compress" "coreshell"
+     "dipole" "granular" "kspace" "manybody" "mc" "misc" "molecule"
+     "opt" "peri" "qeq" "replica" "rigid" "shock" "snap" "srd" "user-reaxc"
+    ];
+    lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
+    withMPI = (mpi != null);
+in
 stdenv.mkDerivation rec {
   # LAMMPS has weird versioning converted to ISO 8601 format
-  version = "patch_2Aug2018";
+  version = "stable_22Aug2018";
   name = "lammps-${version}";
 
-  lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
-  lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
-
   src = fetchFromGitHub {
     owner = "lammps";
     repo = "lammps";
     rev = "${version}";
-    sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
+    sha256 = "1dlifm9wm1jcw2zwal3fnzzl41ng08c7v48w6hx2mz84zljg1nsj";
   };
 
   passthru = {
     inherit mpi;
+    inherit packages;
   };
 
-  buildInputs = [ fftw libpng openblas gzip bash ]
-  ++ (stdenv.lib.optionals mpiSupport [ mpi ]);
+  buildInputs = [ fftw libpng openblas gzip ]
+    ++ (stdenv.lib.optionals withMPI [ mpi ]);
+
+  configurePhase = ''
+    cd src
+    for pack in ${stdenv.lib.concatStringsSep " " packages}; do make "yes-$pack" SHELL=$SHELL; done
+  '';
 
   # Must do manual build due to LAMMPS requiring a seperate build for
-  # the libraries and executable
-  builder = writeText "builder.sh" ''
-    source $stdenv/setup
+  # the libraries and executable. Also non-typical make script
+  buildPhase = ''
+    make mode=exe ${if withMPI then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    make mode=shlib ${if withMPI then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+  '';
 
-    mkdir lammps
-    cp -r $src/lib $src/src lammps
-    chmod -R 755 lammps/src/
-    cd lammps/src
-    for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
-    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
-    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+  installPhase = ''
+    mkdir -p $out/bin $out/include $out/lib
 
-    mkdir -p $out/bin
     cp -v lmp_* $out/bin/
-
-    mkdir -p $out/include
     cp -v *.h $out/include/
-
-    mkdir -p $out/lib
     cp -v liblammps* $out/lib/
   '';
 
-  meta = {
+  meta = with stdenv.lib; {
     description = "Classical Molecular Dynamics simulation code";
     longDescription = ''
       LAMMPS is a classical molecular dynamics simulation code designed to
@@ -67,8 +60,8 @@ stdenv.mkDerivation rec {
       under the terms of the GNU Public License (GPL).
       '';
     homepage = http://lammps.sandia.gov;
-    license = stdenv.lib.licenses.gpl2;
-    platforms = stdenv.lib.platforms.linux;
-    maintainers = with lib.maintainers; [ costrouc ];
+    license = licenses.gpl2;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.costrouc ];
   };
 }
diff --git a/pkgs/applications/science/physics/xfitter/default.nix b/pkgs/applications/science/physics/xfitter/default.nix
index a6ec9960045..833370f8144 100644
--- a/pkgs/applications/science/physics/xfitter/default.nix
+++ b/pkgs/applications/science/physics/xfitter/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, apfel, apfelgrid, applgrid, blas, gfortran, lhapdf, liblapackWithoutAtlas, libyaml, lynx, mela, root5, qcdnum, which }:
+{ stdenv, fetchurl, apfel, apfelgrid, applgrid, blas, gfortran, lhapdf, liblapack, libyaml, lynx, mela, root5, qcdnum, which }:
 
 stdenv.mkDerivation rec {
   name = "xfitter-${version}";
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ gfortran which ];
   buildInputs =
-    [ apfel apfelgrid applgrid blas lhapdf liblapackWithoutAtlas mela root5 qcdnum ]
+    [ apfel apfelgrid applgrid blas lhapdf liblapack mela root5 qcdnum ]
     # pdf2yaml requires fmemopen and open_memstream which are not readily available on Darwin
     ++ stdenv.lib.optional (!stdenv.isDarwin) libyaml
     ;
diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix
index ce3317da9f8..eae5d3766d6 100644
--- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix
+++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix
@@ -37,6 +37,7 @@ stdenv.mkDerivation rec {
     cd ..
 
     mkdir -p $out/share/applications
+    sed 's/Exec=.*$/Exec=QGroundControl/g' --in-place deploy/qgroundcontrol.desktop
     cp -v deploy/qgroundcontrol.desktop $out/share/applications
 
     mkdir -p $out/bin