generated from seqan/app-template
/
CMakeLists.txt
175 lines (142 loc) · 7.48 KB
/
CMakeLists.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
# -----------------------------------------------------------------------------------------------------
# Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
# Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
# shipped with this file and also available at: https://github.com/seqan/raptor/blob/master/LICENSE.md
# -----------------------------------------------------------------------------------------------------
cmake_minimum_required (VERSION 3.11)
# Define the application name and version.
project (raptor VERSION 2.0.1)
# Messages
string (ASCII 27 Esc)
set (FontBold "${Esc}[1m")
set (FontReset "${Esc}[m")
# Fallback to these values if there is no git or no git repository
set (RAPTOR_COMMIT_DATE "2021-08-20--no-git"
CACHE STRING
"Set to provide a commit date if git is not available or the source directory is not a git repository.")
set (RAPTOR_COMMIT_HASH "74f815358db47037e93a56b826a9df3692e55680--no-git"
CACHE STRING
"Set to provide a commit hash if git is not available or the source directory is not a git repository.")
# Extract git commit hash and date
find_package (Git QUIET)
if (GIT_FOUND)
execute_process (COMMAND "${GIT_EXECUTABLE}" -C "${CMAKE_SOURCE_DIR}" rev-parse
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
RESULT_VARIABLE is_no_git_repository
ERROR_QUIET)
if (NOT is_no_git_repository)
execute_process (COMMAND "${GIT_EXECUTABLE}" describe --always --abbrev=40 --dirty
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
OUTPUT_VARIABLE RAPTOR_COMMIT_HASH
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process (COMMAND
"${GIT_EXECUTABLE}" log -1 --format=%ad --date=short
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
OUTPUT_VARIABLE RAPTOR_COMMIT_DATE
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif ()
endif ()
## BUILD
# Make Release default build type
if (NOT CMAKE_BUILD_TYPE)
set (CMAKE_BUILD_TYPE Release CACHE STRING
"Choose the type of build, options are: Debug Release Coverage RelWithDebInfo MinSizeRel."
FORCE)
endif ()
set (RAPTOR_SUBMODULES_DIR "${CMAKE_CURRENT_LIST_DIR}/lib" CACHE STRING "Directory containing submodules.")
include (CheckCXXCompilerFlag)
set (RAPTOR_NATIVE_BUILD ON CACHE BOOL "Optimize build for current architecture.")
if ("${CMAKE_BUILD_TYPE}" MATCHES "Debug" OR "${CMAKE_BUILD_TYPE}" MATCHES "Coverage")
message (STATUS "${FontBold}Native build disabled due to Debug/Coverage build.${FontReset}")
elseif (RAPTOR_NATIVE_BUILD)
message (STATUS "${FontBold}Native build enabled. Built binaries will be optimized for this system.${FontReset}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
else ()
message (STATUS "${FontBold}Native build disabled. Detecting popcnt support.${FontReset}")
check_cxx_compiler_flag ("-mpopcnt" RAPTOR_HAS_POPCNT)
if (RAPTOR_HAS_POPCNT)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
endif ()
endif ()
check_cxx_compiler_flag ("-fopenmp" RAPTOR_HAS_OPENMP)
if (RAPTOR_HAS_OPENMP)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
endif ()
check_cxx_compiler_flag ("-fopenmp-simd" RAPTOR_HAS_OPENMP_SIMD)
if (RAPTOR_HAS_OPENMP_SIMD)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp-simd -DSIMDE_ENABLE_OPENMP")
endif ()
check_cxx_compiler_flag ("-fopenmp-simd" RAPTOR_SUPPRESS_GCC4_ABI)
if (RAPTOR_SUPPRESS_GCC4_ABI)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-psabi")
endif ()
# Specify the directories where to store the built archives, libraries and executables
set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
set (CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
# Dependency: SeqAn3.
set (SEQAN3_CEREAL ON CACHE BOOL "Require cereal to be present.")
set (SEQAN3_SUBMODULES_DIR "${RAPTOR_SUBMODULES_DIR}")
find_package (SeqAn3 QUIET REQUIRED HINTS ${RAPTOR_SUBMODULES_DIR}/seqan3/build_system)
# Define cmake configuration flags to configure and build external projects with the same flags as specified for
# this project.
set (SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_COMPILER_LAUNCHER=${CMAKE_C_COMPILER_LAUNCHER}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_FLAGS=${CMAKE_C_FLAGS}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_COMPILER_LAUNCHER=${CMAKE_CXX_COMPILER_LAUNCHER}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR}")
list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_VERBOSE_MAKEFILE=${CMAKE_VERBOSE_MAKEFILE}")
# Dependency: chopper
set (RAPTOR_CHOPPER_PATH "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/libchopper_count_lib.a")
list (APPEND RAPTOR_CHOPPER_PATH "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/libchopper_layout_lib.a")
if (EXISTS "${RAPTOR_CHOPPER_PATH}")
add_custom_target (chopper_lib)
else ()
set (RAPTOR_CHOPPER_ARGS "${SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS}")
list (APPEND RAPTOR_CHOPPER_ARGS "-DCHOPPER_SUBMODULES_DIR=${RAPTOR_SUBMODULES_DIR}")
list (APPEND RAPTOR_CHOPPER_ARGS "-DSEQAN3_SUBMODULES_DIR=${RAPTOR_SUBMODULES_DIR}")
list (APPEND RAPTOR_CHOPPER_ARGS "-DCMAKE_INSTALL_LIBDIR=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")
list (APPEND RAPTOR_CHOPPER_ARGS "-DCMAKE_INSTALL_BINDIR=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}")
include (ExternalProject)
ExternalProject_Add (
chopper_lib
PREFIX chopper_lib
SOURCE_DIR "${RAPTOR_SUBMODULES_DIR}/chopper"
DOWNLOAD_COMMAND ""
CMAKE_ARGS "${RAPTOR_CHOPPER_ARGS}"
BUILD_BYPRODUCTS "${RAPTOR_CHOPPER_PATH}"
UPDATE_DISCONNECTED 1
)
endif ()
add_library (chopper_count STATIC IMPORTED)
add_dependencies (chopper_count chopper_lib)
set_target_properties (chopper_count PROPERTIES IMPORTED_LOCATION "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/libchopper_count_lib.a")
add_library (chopper_layout STATIC IMPORTED)
add_dependencies (chopper_layout chopper_lib)
set_target_properties (chopper_layout PROPERTIES IMPORTED_LOCATION "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/libchopper_layout_lib.a")
add_library (chopper INTERFACE IMPORTED)
set_property (TARGET chopper PROPERTY INTERFACE_LINK_LIBRARIES chopper_count chopper_layout)
# Allow to include CMake scripts from seqan3.
list (APPEND CMAKE_MODULE_PATH "${SEQAN3_CLONE_DIR}/test/cmake/")
# Use ccache.
set (RAPTOR_USE_CCACHE ON CACHE BOOL "Use ccache if available.")
if (RAPTOR_USE_CCACHE)
include (seqan3_require_ccache)
seqan3_require_ccache ()
endif ()
# Add the application.
add_subdirectory (src)
message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
## DOCUMENTATION
add_subdirectory (doc EXCLUDE_FROM_ALL)
## TEST
set (RAPTOR_ENABLE_BENCHMARK OFF CACHE BOOL "Compile benchmarks as cli tests.")
enable_testing ()
add_subdirectory (test EXCLUDE_FROM_ALL)