Merge remote-tracking branch 'origin/master' into hardened-stdenv

pkgs/development/libraries/science/biology/htslib/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "htslib";
+  version = "1.3.1";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6";
+  };
+
+  buildInputs = [ zlib ];
+
+  meta = with stdenv.lib; {
+    description = "A C library for reading/writing high-throughput sequencing data";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}
+

pkgs/development/libraries/science/math/clblas/cuda/default.nix

@@ -0,0 +1,68 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+, gfortran
+, blas
+, boost
+, python
+, cudatoolkit
+, nvidia_x11
+}:
+
+stdenv.mkDerivation rec {
+  name = "clblas-cuda-${version}"; 
+  version = "git-20160505"; 
+
+  src = fetchFromGitHub {
+    owner = "clMathLibraries"; 
+    repo = "clBLAS";
+    rev = "d20977ec4389c6b3751e318779410007c5e272f8";
+    sha256 = "1jna176cxznv7iz43svd6cjrbbf0fc2lrbpfpg4s08vc7xnwp0n4";
+  }; 
+
+  patches = [ ./platform.patch ]; 
+
+  postPatch = ''
+    sed -i -re 's/(set\(\s*Boost_USE_STATIC_LIBS\s+).*/\1OFF\ \)/g' src/CMakeLists.txt
+  '';
+
+  configurePhase = ''    
+    findInputs ${boost} boost_dirs propagated-native-build-inputs
+
+    export BOOST_INCLUDEDIR=$(echo $boost_dirs | sed -e s/\ /\\n/g - | grep '\-dev')/include
+    export BOOST_LIBRARYDIR=$(echo $boost_dirs | sed -e s/\ /\\n/g - | grep -v '\-dev')/lib
+
+    mkdir -p Build
+    pushd Build
+
+    export LD_LIBRARY_PATH="${blas}/lib:${nvidia_x11}/lib"
+
+    cmake ../src -DCMAKE_INSTALL_PREFIX=$out \
+                 -DCMAKE_BUILD_TYPE=Release \
+                 -DOPENCL_ROOT=${cudatoolkit} \
+  '';
+
+  dontStrip = true; 
+
+  buildInputs = [
+    cmake
+    gfortran
+    blas
+    python
+    cudatoolkit
+    nvidia_x11
+  ]; 
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/clMathLibraries/clBLAS;
+    description = "A software library containing BLAS functions written in OpenCL";
+    longDescription = ''
+      This package contains a library of BLAS functions on top of OpenCL. 
+      The current version is linked to the NVIDIA OpenCL implementation provided by the CUDA toolkit. 
+    '';
+    license = licenses.asl20;
+    maintainers = with maintainers; [ artuuge ];
+    platforms = platforms.linux;
+  };
+
+}

pkgs/development/libraries/science/math/clblas/cuda/platform.patch

@@ -0,0 +1,34 @@
+diff --git a/src/library/tools/ktest/config.cpp b/src/library/tools/ktest/config.cpp
+index 8b20128..faf9bde 100644
+--- a/src/library/tools/ktest/config.cpp
++++ b/src/library/tools/ktest/config.cpp
+@@ -24,8 +24,6 @@
+ 
+ using namespace clMath;
+ 
+-static const char DEFAULT_PLATFORM_NAME[] = "AMD Accelerated Parallel Processing";
+-
+ Config::Config() :
+     defaultConfig_(""),
+     cpp_("ktest.cpp"),
+@@ -35,7 +33,10 @@ Config::Config() :
+     hasFuncID_(false), hasSubdims_(false),
+     skipAccuracy_(false)
+ {
+-    setPlatform(DEFAULT_PLATFORM_NAME);
++    platform_ = NULL;
++    setPlatform("");
++
++    device_ = NULL;
+     setDevice("");
+ 
+     memset(&kargs_, 0, sizeof(kargs_));
+@@ -262,7 +263,7 @@ Config::setPlatform(const std::string& name)
+             continue;
+         }
+         if (name.empty()) {
+-            found = (strcmp(pname, DEFAULT_PLATFORM_NAME) == 0);
++	    found = true;
+         }
+         else {
+             found = (strcmp(pname, name.c_str()) == 0);

pkgs/development/libraries/science/math/cudnn/7.5-5.0/default.nix

@@ -0,0 +1,46 @@
+{ stdenv
+, requireFile
+, cudatoolkit
+}:
+
+stdenv.mkDerivation rec {
+  version = "5.0";
+  cudatoolkit_version = "7.5";
+
+  name = "cudatoolkit-${cudatoolkit_version}-cudnn-${version}";
+
+  src = requireFile rec {
+    name = "cudnn-${cudatoolkit_version}-linux-x64-v${version}-ga.tgz";
+    message = ''
+      This nix expression requires that ${name} is already part of the store.
+      Register yourself to NVIDIA Accelerated Computing Developer Program, retrieve the cuDNN library
+      at https://developer.nvidia.com/cudnn, and run the following command in the download directory:
+      nix-prefetch-url file://${name}
+    '';
+    sha256 = "c4739a00608c3b66a004a74fc8e721848f9112c5cb15f730c1be4964b3a23b3a";
+  };
+
+  phases = "unpackPhase installPhase fixupPhase";
+
+  installPhase = ''
+    function fixRunPath {
+      p=$(patchelf --print-rpath $1)
+      patchelf --set-rpath "$p:${stdenv.lib.makeLibraryPath [ stdenv.cc.cc ]}" $1
+    }
+    fixRunPath lib64/libcudnn.so
+
+    mkdir -p $out
+    cp -a include $out/include
+    cp -a lib64 $out/lib64
+  '';
+
+  propagatedBuildInputs = [
+    cudatoolkit
+  ];
+
+  meta = {
+    description = "NVIDIA CUDA Deep Neural Network library (cuDNN)";
+    homepage = "https://developer.nvidia.com/cudnn";
+    license = stdenv.lib.licenses.unfree;
+  };
+}