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| author | markuskowa <markus.kowalewski@gmail.com> | 2021-12-03 21:55:44 +0100 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-12-03 21:55:44 +0100 |
| commit | 0016232876c0227545a9b9600d62c0f56705e0cc (patch) | |
| tree | d0725e3cbdcd39caff179289b4969e548e0be877 /pkgs/applications/science | |
| parent | e1fb73a3f2482869ebf3b36a4e33dbeedccf0331 (diff) | |
| parent | 1a768ef4da5450ce3e5afad447d238c54e66d103 (diff) | |
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Merge pull request #148350 from jbedo/genmap
genmap: init 1.3.0
Diffstat (limited to 'pkgs/applications/science')
| -rw-r--r-- | pkgs/applications/science/biology/genmap/default.nix | 40 | ||||
| -rw-r--r-- | pkgs/applications/science/biology/genmap/gtest.patch | 30 |
2 files changed, 70 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/genmap/default.nix b/pkgs/applications/science/biology/genmap/default.nix new file mode 100644 index 00000000000..c2d1b8da7af --- /dev/null +++ b/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${version}"; + fetchSubmodules = true; + sha256 = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY="; + }; + + nativeBuildInputs = [ cmake ]; + + doCheck = true; + patches = [ ./gtest.patch ]; + checkInputs = [ gtest which ]; + preCheck = "make genmap_algo_test"; + + # disable benchmarks + preConfigure = '' + echo > benchmarks/CMakeLists.txt + ''; + + meta = { + description = "Ultra-fast computation of genome mappability"; + license = lib.licenses.bsd3; + homepage = "https://github.com/cpockrandt/genmap"; + maintainers = with lib.maintainers; [ jbedo ]; + platforms = lib.platforms.unix; + }; +} diff --git a/pkgs/applications/science/biology/genmap/gtest.patch b/pkgs/applications/science/biology/genmap/gtest.patch new file mode 100644 index 00000000000..f01d0e115eb --- /dev/null +++ b/pkgs/applications/science/biology/genmap/gtest.patch @@ -0,0 +1,30 @@ +diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt +index 67ec8f9..ed0b2e0 100644 +--- a/tests/CMakeLists.txt ++++ b/tests/CMakeLists.txt +@@ -2,23 +2,14 @@ + # GenMap tests + # =========================================================================== + +-include (ExternalProject) +-ExternalProject_Add (googletest +- PREFIX "${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) |