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-rw-r--r--pkgs/applications/science/biology/last/default.nix30
-rw-r--r--pkgs/applications/science/biology/minia/default.nix33
-rw-r--r--pkgs/applications/science/biology/minia/no-bundle.patch222
-rw-r--r--pkgs/applications/science/biology/tebreak/default.nix42
-rw-r--r--pkgs/applications/science/chemistry/jmol/default.nix4
-rw-r--r--pkgs/applications/science/logic/aspino/default.nix2
-rw-r--r--pkgs/applications/science/math/sage/sage-src.nix7
-rw-r--r--pkgs/applications/science/misc/openmodelica/default.nix4
-rw-r--r--pkgs/applications/science/misc/root/default.nix14
-rw-r--r--pkgs/applications/science/robotics/mavproxy/default.nix4
10 files changed, 352 insertions, 10 deletions
diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix
new file mode 100644
index 00000000000..5ece9a463d4
--- /dev/null
+++ b/pkgs/applications/science/biology/last/default.nix
@@ -0,0 +1,30 @@
+{ stdenv, fetchurl, unzip, zlib, python3, parallel }:
+
+stdenv.mkDerivation rec {
+  pname = "last";
+  version = "1042";
+
+  src = fetchurl {
+    url = "http://last.cbrc.jp/last-${version}.zip";
+    sha256 = "0mgbhd01m9riqza2gx56qk6x5682kg71zflhisr6d3q05wrv103f";
+  };
+
+  nativeBuildInputs = [ unzip ];
+  buildInputs = [ zlib python3 ];
+
+  makeFlags = [ "prefix=${placeholder "out"}" ];
+
+  postFixup = ''
+    for f in $out/bin/parallel-* ; do
+      sed -i 's|parallel |${parallel}/bin/parallel |' $f
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Genomic sequence aligner";
+    homepage = "http://last.cbrc.jp/";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/applications/science/biology/minia/default.nix b/pkgs/applications/science/biology/minia/default.nix
new file mode 100644
index 00000000000..2a80de733b0
--- /dev/null
+++ b/pkgs/applications/science/biology/minia/default.nix
@@ -0,0 +1,33 @@
+{ stdenv, fetchFromGitHub, cmake, hdf5, boost }:
+
+stdenv.mkDerivation rec {
+  pname = "minia";
+  version = "3.2.1";
+
+  src = fetchFromGitHub {
+    owner = "GATB";
+    repo = "minia";
+    rev = "v${version}";
+    sha256 = "0bmfrywixaaql898l0ixsfkhxjf2hb08ssnqzlzacfizxdp46siq";
+    fetchSubmodules = true;
+  };
+
+  patches = [ ./no-bundle.patch ];
+
+  NIX_CFLAGS_COMPILE = [ "-Wformat" ];
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ hdf5 boost ];
+
+  prePatch = ''
+    rm -rf thirdparty/gatb-core/gatb-core/thirdparty/{hdf5,boost}
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Short read genome assembler";
+    homepage = "https://github.com/GATB/minia";
+    license = licenses.agpl3;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
diff --git a/pkgs/applications/science/biology/minia/no-bundle.patch b/pkgs/applications/science/biology/minia/no-bundle.patch
new file mode 100644
index 00000000000..21d12c7f6f2
--- /dev/null
+++ b/pkgs/applications/science/biology/minia/no-bundle.patch
@@ -0,0 +1,222 @@
+diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+index f48a70b..0e11ece 100644
+--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt
++++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty)
+ #  DEPENDENCIES 
+ ################################################################################
+ # we must be sure that hdf5 is built and installed before building gatb-core
+-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
+ 
+ ################################################################################
+ #  DOCUMENTATION GENERATION 
+@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt  DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE              DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md      DESTINATION . OPTIONAL)
+-    INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
+ ENDIF()
+ 
+ ################################################################################
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+index dfeee1c..d5553a2 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+@@ -35,7 +35,7 @@
+ #include <stdint.h>
+ #include <algorithm>
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/Exception.hpp>
+ #include <gatb/system/api/config.hpp>
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+index 60be5d5..25ae75e 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+@@ -33,7 +33,7 @@
+ /********************************************************************************/
+ 
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+index 6a71bb0..b9205df 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+index c22b892..62e6586 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+index c06aaab..e0befba 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ extern const unsigned char revcomp_4NT[];
+ extern const unsigned char comp_NT    [];
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+index 9659874..0c79ff6 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+index 3cb84f8..cd5d382 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+@@ -31,7 +31,7 @@
+ /********************************************************************************/
+ 
+ #include <sys/types.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+index b8f6c79..a040832 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+@@ -28,7 +28,7 @@
+ 
+ #include <gatb/system/api/ISmartPointer.hpp>
+ #include <gatb/tools/storage/impl/Storage.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+index 2645abd..fad48c0 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+index a92b729..66d552f 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+index 29e0949..0565cc4 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+@@ -33,7 +33,7 @@
+ #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
+ #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
+ #include <gatb/system/impl/System.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ #include <sstream>
+ 
+ /********************************************************************************/
+diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+index 6e0b5c4..34aef28 100644
+--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
++++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+@@ -1,54 +1,3 @@
+-################################################################################
+-#  HDF5 GENERATION 
+-################################################################################
+-
+-#SET (HDF5_ENABLE_THREADSAFE       ON)
+-#SET (H5_HAVE_THREADSAFE 1)
+-
+-##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
+-SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
+-#SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
+-
+-SET (HDF5_EXTERNALLY_CONFIGURED     ON)
+-
+-#SET (HDF5_INSTALL_BIN_DIR           ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
+-#SET (HDF5_INSTALL_LIB_DIR           ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_BIN_DIR           bin)
+-SET (HDF5_INSTALL_LIB_DIR           lib)
+-
+-SET (HDF5_INSTALL_INCLUDE_DIR       ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
+-SET (HDF5_INSTALL_DATA_DIR          ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_CMAKE_DIR         ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-
+-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+-    SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
+-ENDIF()
+-
+-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
+-	OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
+-ENDIF()
+-
+-# We don't want warnings from HDF5 compilation
+-set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
+-add_definitions (${COMPILE_DEFINITIONS})
+-
+-# add HDF5 generation
+-ADD_SUBDIRECTORY (hdf5)
+-
+-# We add a custom target for copying header files.
+-add_custom_target (hdf5_postbuild ALL)
+-
+-# We build the output directory
+-add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
+-
+-# We define all the header files to be copied
+-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
+-
+-# We copy each header file
+-foreach (header ${headerfiles})
+-  add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR}  )
+-endforeach()
+-
+ # include other smaller libraries (json, Boophf)
+ 
+ add_custom_target (thirdparty_copy ALL)
diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix
new file mode 100644
index 00000000000..9ff81944f6a
--- /dev/null
+++ b/pkgs/applications/science/biology/tebreak/default.nix
@@ -0,0 +1,42 @@
+{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
+, samtools, findutils }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "tebreak";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "adamewing";
+    repo = "tebreak";
+    rev = version;
+    sha256 = "194av17wz66n4zxyi56mbkik31j2wmkly5i9qmxgaxymhavzi3kq";
+  };
+
+  nativeBuildInputs = [ findutils python3Packages.cython ];
+  propagatedBuildInputs = with python3Packages; [
+    pysam
+    scipy
+    bx-python
+    scikit-bio
+  ];
+
+  preConfigure = ''
+    # patch the paths to all required software
+    for f in $(find . -type f) ; do
+      sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f
+      sed -i "s|'minia'|'${minia}/bin/minia'|" $f
+      sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f
+      sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f
+      sed -i "s|'lastal'|'${last}/bin/lastal'|" $f
+      sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Find and characterise transposable element insertions";
+    homepage = "https://github.com/adamewing/tebreak";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index 3ec127e7e06..2577b2a16e6 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.30.0";
+  version = "14.30.1";
   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 = "0g0pykdp9xgvc485c89lwajy5wgrz66w1n6pqan1v1i4zfbz9vna";
+    sha256 = "0qnxsw6pjjkn6yigrfh85fz58ibqdmbv1jhf6i5q68wm5pr1ff3d";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/logic/aspino/default.nix b/pkgs/applications/science/logic/aspino/default.nix
index 6af7eaf3a5b..82458d7c566 100644
--- a/pkgs/applications/science/logic/aspino/default.nix
+++ b/pkgs/applications/science/logic/aspino/default.nix
@@ -40,7 +40,7 @@ stdenv.mkDerivation {
 
   meta = with stdenv.lib; {
     description = "SAT/PseudoBoolean/MaxSat/ASP solver using glucose";
-    maintainers = with maintainers; [ gebner ma27 ];
+    maintainers = with maintainers; [ gebner ];
     platforms = platforms.unix;
     license = licenses.asl20;
     homepage = https://alviano.net/software/maxino/;
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index dc8ba48e45e..4530cbf69f4 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -118,6 +118,13 @@ stdenv.mkDerivation rec {
       url = "https://git.sagemath.org/sage.git/patch?id=fcc11d6effa39f375bc5f4ea5831fb7a2f2767da";
       sha256 = "0hnmc8ld3bblks0hcjvjjaydkgwdr1cs3dbl2ys4gfq964pjgqwc";
     })
+
+    # https://trac.sagemath.org/ticket/28911
+    (fetchpatch {
+      name = "sympy-1.5.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?h=c6d0308db15efd611211d26cfcbefbd180fc0831";
+      sha256 = "0nwai2jr22h49km4hx3kwafs3mzsc5kwsv7mqwjf6ibwfx2bbgyq";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
diff --git a/pkgs/applications/science/misc/openmodelica/default.nix b/pkgs/applications/science/misc/openmodelica/default.nix
index 1a1ae3df942..ed4101bdb47 100644
--- a/pkgs/applications/science/misc/openmodelica/default.nix
+++ b/pkgs/applications/science/misc/openmodelica/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchgit, fetchsvn, autoconf, automake, libtool, gfortran, clang, cmake, gnumake,
 hwloc, jre, liblapack, blas, hdf5, expat, ncurses, readline, qt4, webkitgtk, which,
 lp_solve, omniorb, sqlite, libatomic_ops, pkgconfig, file, gettext, flex, bison,
-doxygen, boost, openscenegraph, gnome2, pangox_compat, xorg, git, bash, gtk2, makeWrapper }:
+doxygen, boost, openscenegraph, gnome2, xorg, git, bash, gtk2, makeWrapper }:
 
 let
 
@@ -17,7 +17,7 @@ stdenv.mkDerivation {
   buildInputs = [autoconf cmake automake libtool gfortran clang gnumake
     hwloc jre liblapack blas hdf5 expat ncurses readline qt4 webkitgtk which
     lp_solve omniorb sqlite libatomic_ops pkgconfig file gettext flex bison
-    doxygen boost openscenegraph gnome2.gtkglext pangox_compat xorg.libXmu
+    doxygen boost openscenegraph gnome2.gtkglext xorg.libXmu
     git gtk2 makeWrapper];
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix
index 7a03369febe..b901e40a194 100644
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@@ -1,5 +1,6 @@
-{ stdenv, fetchurl, cmake, gl2ps, gsl, libX11, libXpm, libXft, libXext
-, libGLU, libGL, libxml2, lz4, lzma, pcre, pkgconfig, python, xxHash, zlib
+{ stdenv, fetchurl, makeWrapper, cmake, gl2ps, gsl, libX11, libXpm, libXft
+, libXext, libGLU, libGL, libxml2, lz4, lzma, pcre, pkgconfig, python, xxHash
+, zlib
 , Cocoa, OpenGL, noSplash ? false }:
 
 stdenv.mkDerivation rec {
@@ -11,7 +12,7 @@ stdenv.mkDerivation rec {
     sha256 = "196ghma6g5a7sqz52wyjkgvmh4hj4vqwppm0zwdypy33hgy8anii";
   };
 
-  nativeBuildInputs = [ cmake pkgconfig ];
+  nativeBuildInputs = [ makeWrapper cmake pkgconfig ];
   buildInputs = [ gl2ps pcre python zlib libxml2 lz4 lzma gsl xxHash ]
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
     ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
@@ -73,6 +74,13 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  postInstall = ''
+    for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do
+      wrapProgram "$out/bin/$prog" \
+        --prefix PYTHONPATH : "$out/lib"
+    done
+  '';
+
   setupHook = ./setup-hook.sh;
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/robotics/mavproxy/default.nix b/pkgs/applications/science/robotics/mavproxy/default.nix
index 890e824cf2e..0348d015309 100644
--- a/pkgs/applications/science/robotics/mavproxy/default.nix
+++ b/pkgs/applications/science/robotics/mavproxy/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonApplication rec {
   pname = "MAVProxy";
-  version = "1.8.17";
+  version = "1.8.18";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "193hjilsmbljbgj7v6icy3b4hzm14l0z6v05v7ycx6larij5xj2r";
+    sha256 = "1fi4m3591wws5cq43q8aljf91mzs6i9yhn9rimhpfrskbyf9knvm";
   };
 
   propagatedBuildInputs = [