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| author | Toyohisa Kameyama <kameyama@riken.jp> | 2019-10-22 08:38:05 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-10-21 18:38:05 -0500 |
| commit | 98c0d59a0c9963286fb5eb0cdbc63f3a8321916a (patch) | |
| tree | fa33c52c65449c3cb0978846e87514455c3abc5b | |
| parent | 7b62b64b031f27a5317818f0246f9bb844862b39 (diff) | |
| download | spack-98c0d59a0c9963286fb5eb0cdbc63f3a8321916a.tar.gz spack-98c0d59a0c9963286fb5eb0cdbc63f3a8321916a.tar.bz2 spack-98c0d59a0c9963286fb5eb0cdbc63f3a8321916a.tar.xz spack-98c0d59a0c9963286fb5eb0cdbc63f3a8321916a.zip | |
sniffles: fix zlib header lookup directory. (#13063)
* sniffles: fix zlib header lookup directory.
* use bamtools and zlib to spack installed package.
* remove unneeded patch.
| -rw-r--r-- | var/spack/repos/builtin/packages/sniffles/package.py | 9 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/sniffles/unused_libs.patch | 41 |
2 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py index 03da487df1..b6dca88203 100644 --- a/var/spack/repos/builtin/packages/sniffles/package.py +++ b/var/spack/repos/builtin/packages/sniffles/package.py @@ -15,6 +15,15 @@ class Sniffles(CMakePackage): version('1.0.7', sha256='03fa703873bdf9c32055c584448e1eece45f94b4bc68e60c9624cf3841e6d8a9') version('1.0.5', sha256='386c6536bdaa4637579e235bac48444c08297337c490652d1e165accd34b258f') + depends_on('zlib', type='link') + depends_on('bamtools', type='link') + + patch('unused_libs.patch') + + def cmake_args(self): + i = self.spec['bamtools'].prefix.include.bamtools + return ['-DCMAKE_CXX_FLAGS=-I{0}'.format(i)] + # the build process doesn't actually install anything, do it by hand def install(self, spec, prefix): mkdir(prefix.bin) diff --git a/var/spack/repos/builtin/packages/sniffles/unused_libs.patch b/var/spack/repos/builtin/packages/sniffles/unused_libs.patch new file mode 100644 index 0000000000..3a1813c454 --- /dev/null +++ b/var/spack/repos/builtin/packages/sniffles/unused_libs.patch @@ -0,0 +1,41 @@ +--- spack-src.org/CMakeLists.txt 2017-11-14 04:24:46.000000000 +0900 ++++ spack-src/CMakeLists.txt 2019-10-08 09:10:10.409449275 +0900 +@@ -29,8 +29,4 @@ + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") + endif() + +- +-add_subdirectory(lib/zlib-1.2.7) +-add_subdirectory(lib/bamtools-2.3.0) +- + add_subdirectory(src) +--- spack-src.org/src/CMakeLists.txt 2017-11-14 04:24:46.000000000 +0900 ++++ spack-src/src/CMakeLists.txt 2019-10-08 09:21:52.569644934 +0900 +@@ -1,7 +1,6 @@ + cmake_minimum_required(VERSION 2.8) + project(Sniffles) + +-include_directories (../lib/bamtools-2.3.0/src) + include_directories(../lib/tclap-1.2.1/include) + + configure_file( Version.h.in ${CMAKE_SOURCE_DIR}/src/Version.h ) +@@ -32,8 +31,8 @@ + ) + + #target_link_libraries(ngm-core pthread) +-TARGET_LINK_LIBRARIES(sniffles BamTools-static) +-TARGET_LINK_LIBRARIES(sniffles zlibstatic) ++TARGET_LINK_LIBRARIES(sniffles bamtools) ++TARGET_LINK_LIBRARIES(sniffles z) + + add_executable(sniffles-debug + tree/Breakpoint_Tree.cpp +@@ -63,6 +62,6 @@ + SET_TARGET_PROPERTIES(sniffles-debug PROPERTIES COMPILE_FLAGS "-g3 -O0") + + #target_link_libraries(sniffles-debug pthread) +-TARGET_LINK_LIBRARIES(sniffles-debug BamTools-static) +-TARGET_LINK_LIBRARIES(sniffles-debug zlibstatic) ++TARGET_LINK_LIBRARIES(sniffles-debug bamtools) ++TARGET_LINK_LIBRARIES(sniffles-debug z) + |