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sniffles: fix zlib header lookup directory. (#13063)

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* sniffles: fix zlib header lookup directory.

* use bamtools and zlib to spack installed package.

* remove unneeded patch.
This commit is contained in:
Toyohisa Kameyama 2019-10-22 08:38:05 +09:00 committed by Adam J. Stewart
parent 7b62b64b03
commit 98c0d59a0c
2 changed files with 50 additions and 0 deletions
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9
var/spack/repos/builtin/packages/sniffles/package.py
View File

@ -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)

41
var/spack/repos/builtin/packages/sniffles/unused_libs.patch Normal file
View File

@ -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)