soedinglab compatibility: Add CMakeLists.txt

CMakeLists.txt

@@ -0,0 +1,8 @@
+cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
+SET(HAVE_MPI 1 CACHE BOOL "Have MPI")
+
+project(ffindex C)
+include_directories(src)
+include_directories(src/ext)
+add_subdirectory(src)
+

src/CMakeLists.txt

@@ -0,0 +1,102 @@
+set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")
+
+# sets HAVE_FMEMOPEN
+add_subdirectory(ext)
+
+add_library (ffindex ffindex.c ffutil.c ffindex_posix_search.c)
+
+target_include_directories (ffindex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+
+add_library (ffindex_shared SHARED ffindex.c ffutil.c)
+
+if(NOT HAVE_FMEMOPEN)
+        target_link_libraries(ffindex ext)
+        target_link_libraries(ffindex_shared ext)
+endif()
+
+
+
+add_executable(ffindex_apply
+        ffindex_apply_mpi.c
+)
+target_link_libraries (ffindex_apply ffindex)
+set_property(TARGET ffindex_apply PROPERTY COMPILE_FLAGS "-UHAVE_MPI")
+
+find_package(MPI)
+if(MPI_C_FOUND AND HAVE_MPI)
+    add_executable(ffindex_apply_mpi
+      ffindex_apply_mpi.c
+    )
+    target_link_libraries (ffindex_apply_mpi ffindex)
+    add_subdirectory(mpq)
+
+    set_property(TARGET ffindex_apply_mpi PROPERTY COMPILE_FLAGS "-DHAVE_MPI=1 ${MPI_C_COMPILE_FLAGS}")
+    set_property(TARGET ffindex_apply_mpi PROPERTY LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+
+    target_include_directories(ffindex_apply_mpi PUBLIC ${MPI_C_INCLUDE_PATH})
+    target_link_libraries (ffindex_apply_mpi mpq ${MPI_C_LIBRARIES})
+    install(TARGETS
+        ffindex_apply_mpi
+        DESTINATION bin
+    )
+endif()
+
+
+add_executable(ffindex_build
+  ffindex_build.c
+)
+target_link_libraries (ffindex_build ffindex)
+
+
+add_executable(ffindex_from_fasta
+  ffindex_from_fasta.c
+)
+target_link_libraries (ffindex_from_fasta ffindex)
+
+
+add_executable(ffindex_get
+  ffindex_get.c
+)
+target_link_libraries (ffindex_get ffindex)
+
+
+add_executable(ffindex_modify
+  ffindex_modify.c
+)
+target_link_libraries (ffindex_modify ffindex)
+
+
+add_executable(ffindex_unpack
+  ffindex_unpack.c
+)
+target_link_libraries (ffindex_unpack ffindex)
+
+
+install(PROGRAMS 
+        ffindex.h 
+        ffutil.h
+        DESTINATION include
+)
+
+install(TARGETS ffindex
+  LIBRARY DESTINATION lib64 COMPONENT libraries
+        ARCHIVE DESTINATION lib64 COMPONENT libraries
+)
+
+
+install(TARGETS ffindex_shared
+  LIBRARY DESTINATION lib64 COMPONENT libraries
+        ARCHIVE DESTINATION lib64 COMPONENT libraries
+)
+
+
+INSTALL( 
+  TARGETS
+  ffindex_apply
+  ffindex_build
+  ffindex_from_fasta
+  ffindex_get
+  ffindex_modify
+  ffindex_unpack
+  DESTINATION bin
+)

src/ext/CMakeLists.txt

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+### fmemopen
+include (${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
+check_function_exists(fmemopen HAVE_FMEMOPEN)
+
+if(NOT HAVE_FMEMOPEN)
+set(EXT_SRC
+
+  fmemopen.c
+  fmemopen.h
+)
+add_library(ext ${EXT_SRC})
+endif()