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authorToyohisa Kameyama <kameyama@riken.jp>2019-10-22 08:38:05 +0900
committerAdam J. Stewart <ajstewart426@gmail.com>2019-10-21 18:38:05 -0500
commit98c0d59a0c9963286fb5eb0cdbc63f3a8321916a (patch)
treefa33c52c65449c3cb0978846e87514455c3abc5b
parent7b62b64b031f27a5317818f0246f9bb844862b39 (diff)
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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.py9
-rw-r--r--var/spack/repos/builtin/packages/sniffles/unused_libs.patch41
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)
+