genmap: init 1.3.0

pkgs/applications/science/biology/genmap/default.nix

@@ -0,0 +1,40 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, gtest
+, which
+}:
+
+stdenv.mkDerivation rec {
+  pname = "genmap";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "cpockrandt";
+    repo = "genmap";
+    rev = "genmap-v${version}";
+    fetchSubmodules = true;
+    sha256 = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  doCheck = true;
+  patches = [ ./gtest.patch ];
+  checkInputs = [ gtest which ];
+  preCheck = "make genmap_algo_test";
+
+  # disable benchmarks
+  preConfigure = ''
+    echo > benchmarks/CMakeLists.txt
+  '';
+
+  meta = {
+    description = "Ultra-fast computation of genome mappability";
+    license = lib.licenses.bsd3;
+    homepage = "https://github.com/cpockrandt/genmap";
+    maintainers = with lib.maintainers; [ jbedo ];
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/applications/science/biology/genmap/gtest.patch

@@ -0,0 +1,30 @@
+diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
+index 67ec8f9..ed0b2e0 100644
+--- a/tests/CMakeLists.txt
++++ b/tests/CMakeLists.txt
+@@ -2,23 +2,14 @@
+ #  GenMap tests
+ # ===========================================================================
+ 
+-include (ExternalProject)
+-ExternalProject_Add (googletest
+-                     PREFIX "${CMAKE_CURRENT_BINARY_DIR}/googletest"
+-                     GIT_REPOSITORY "https://github.com/google/googletest.git"
+-                     INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}"
+-                     CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}"
+-                     GIT_TAG release-1.10.0
+-                     UPDATE_DISCONNECTED YES)
+ 
+ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") # TODO: --coverage
+ add_executable (genmap_algo_test tests.cpp)
+-add_dependencies (genmap_algo_test googletest)
+ 
+ include_directories (${CMAKE_CURRENT_BINARY_DIR}/include)
+ target_link_libraries (genmap_algo_test ${SEQAN_LIBRARIES})
+-target_link_libraries (genmap_algo_test ${CMAKE_CURRENT_BINARY_DIR}/lib/libgtest.a)
+-target_link_libraries (genmap_algo_test ${CMAKE_CURRENT_BINARY_DIR}/lib/libgtest_main.a)
++target_link_libraries (genmap_algo_test -lgtest)
++target_link_libraries (genmap_algo_test -lgtest_main)
+ target_link_libraries (genmap_algo_test pthread)
+ 
+ add_test(NAME algo_test COMMAND genmap_algo_test)

pkgs/top-level/all-packages.nix

@@ -5507,6 +5507,8 @@ with pkgs;
 
   genimage = callPackage ../tools/filesystems/genimage { };
 
+  genmap = callPackage ../applications/science/biology/genmap { };
+
   geonkick = callPackage ../applications/audio/geonkick {};
 
   gerrit = callPackage ../applications/version-management/gerrit { };