forked from yatisht/usher
-
Notifications
You must be signed in to change notification settings - Fork 0
/
CMakeLists.txt
522 lines (474 loc) · 20.1 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
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
cmake_minimum_required (VERSION 3.8)
cmake_policy(SET CMP0069 NEW)
project(usher)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "RelWithDebInfo")
endif()
set(usher_VERSION "?.?.?")
find_library(ISAL_LIB isal)
execute_process(COMMAND head -n1 ${CMAKE_SOURCE_DIR}/version.txt OUTPUT_VARIABLE VERSION)
string(REGEX REPLACE "^v([0-9]+)\\..*" "\\1" VERSION_MAJOR "${VERSION}")
string(REGEX REPLACE "^v[0-9]+\\.([0-9]+).*" "\\1" VERSION_MINOR "${VERSION}")
string(REGEX REPLACE "^v[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" VERSION_PATCH "${VERSION}")
if ("${VERSION_PATCH}" MATCHES "[0-9]+")
set(usher_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
endif()
message(STATUS "${usher_VERSION}")
configure_file(src/version.hpp.in version.hpp)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -Wall -pipe -g -ggdb3 -Wno-unused-function -Wno-deprecated-declarations")
#-DDEBUG_PARSIMONY_SCORE_CHANGE_CORRECT -fsanitize=address -DCHECK_PAR_MAIN -DEASY_DEBUG -DSTOP_ON_ERROR -DDETAILED_MERGER_CHECK -O0
set(CMAKE_CXX_FLAGS_DEBUG " -fno-eliminate-unused-debug-symbols -O0")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-DNDEBUG -O3")
set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 ")
set(CMAKE_INCLUDE_CURRENT_DIR ON)
if(DEFINED Protobuf_PATH)
find_package(Protobuf REQUIRED HINTS ${Protobuf_PATH})
else()
find_package(Protobuf REQUIRED)
endif()
# Print version messages
if(Protobuf_FOUND)
message(STATUS "Using Protocol Buffers ${Protobuf_VERSION}")
endif()
find_package(MPI REQUIRED)
include_directories(SYSTEM ${MPI_INCLUDE_PATH})
include_directories(${Protobuf_INCLUDE_DIRS})
include(${TBB_DIR}/cmake/TBBBuild.cmake)
tbb_build(TBB_ROOT ${TBB_DIR} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1)
find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview)
FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED)
#find_package(OpenMP REQUIRED)
INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
AUX_SOURCE_DIRECTORY(src/matOptimize/Profitable_Moves_Enumerators New_Profitable_Moves_Enumerators)
AUX_SOURCE_DIRECTORY(src/matOptimize/apply_move patch_tree)
AUX_SOURCE_DIRECTORY(src/check_samples_place check_samples_place)
file(GLOB MATUTIL_SRCS "src/matUtils/*.cpp" "src/matUtils/*.hpp")
file(GLOB RIPPLES_SRCS "src/ripples/*.cpp" "src/ripples/*.hpp")
file(GLOB USHER_SAMPLED_SRCS "src/usher-sampled/static_tree_mapper/*" "src/usher-sampled/*.cpp" "src/usher-sampled/*.hpp")
file(GLOB RIPPLES_FAST_SRCS "src/ripples/ripples_fast/*.cpp" "src/ripples/ripples_fast/*.hpp")
file(GLOB RIPPLES_UTILS_SRCS "src/ripples/util/*.cpp" "src/ripples/util/*.hpp")
set_source_files_properties(src/mutation_annotated_tree.cpp PROPERTIES COMPILE_FLAGS -O3)
set_source_files_properties(src/usher-sampled/wait_debug.cpp PROPERTIES COMPILE_FLAGS -O0)
#set_source_files_properties(src/matOptimize/Profitable_Moves_Enumerators/range_tree.cpp PROPERTIES COMPILE_FLAGS -O0)
#set_source_files_properties(src/matOptimize/detailed_mutations_store.cpp PROPERTIES COMPILE_FLAGS -O0)
#set_source_files_properties(src/matOptimize/detailed_mutations_load.cpp PROPERTIES COMPILE_FLAGS -O0)
#set_source_files_properties(src/matOptimize/serializer_test.cpp PROPERTIES COMPILE_FLAGS -O0)
find_package(ZLIB)
if(DEFINED Protobuf_PATH)
add_executable(usher
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/usher_common.cpp
src/usher.cpp
)
add_executable(matUtils
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${MATUTIL_SRCS}
)
add_executable(ripples
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${RIPPLES_SRCS}
)
add_executable(ripples-fast
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${RIPPLES_FAST_SRCS}
)
add_executable(usher-sampled
${USHER_SAMPLED_SRCS}
src/matOptimize/main_helper.cpp
src/matOptimize/detailed_mutations_store.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/check_samples.cpp
src/matOptimize/optimize_tree.cpp
src/matOptimize/condense.cpp
src/matOptimize/Fitch_Sankoff.cpp
src/matOptimize/main_load_tree.cpp
src/matOptimize/priority_conflict_resolver.cpp
src/usher-sampled/driver/main.cpp
${patch_tree}
${New_Profitable_Moves_Enumerators}
)
add_executable(ripplesUtils
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/matUtils/describe.cpp
${RIPPLES_UTILS_SRCS}
)
add_executable(ripplesInit
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/ripples/init/init_pipeline.cpp
src/ripples/init/main.cpp
)
add_executable(matOptimize
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/detailed_mutations_store.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/main.cpp
src/matOptimize/optimize_tree.cpp
src/matOptimize/import_vcf_fast.cpp
src/matOptimize/condense.cpp
src/matOptimize/optimize_inner_loop.cpp
src/matOptimize/VCF_load_tree.cpp
src/matOptimize/main_load_tree.cpp
src/matOptimize/main_helper.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/Fitch_Sankoff.cpp
src/matOptimize/check_samples.cpp
#src/matOptimize/priority_conflict_resolver_cross_only.cpp
src/matOptimize/priority_conflict_resolver.cpp
src/matOptimize/transpose_vcf/transposed_vcf_patch.cpp
${patch_tree}
${New_Profitable_Moves_Enumerators}
)
add_executable(compareVCF
src/mutation_annotated_tree.cpp
src/compareVCF.cpp
src/usher_mapper.cpp
)
add_executable(output_final_protobuf
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/main_helper.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/output_final_protobuf.cpp
)
add_executable(transpose_vcf
src/matOptimize/transpose_vcf/transpose_vcf_encode.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
add_executable(transposed_vcf_to_vcf
src/matOptimize/transpose_vcf/transposed_vcf_to_vcf.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
add_executable(transposed_vcf_to_fa
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/transpose_vcf/transposed_vcf_to_fa.cpp
)
add_executable(transposed_vcf_print_name
src/matOptimize/transpose_vcf/transposed_vcf_print_name.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
if(USHER_SERVER)
add_executable(usher_server
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/usher_common.cpp
src/usher_server.cpp
)
endif()
protobuf_generate(
LANGUAGE cpp
TARGET ripples
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET ripples-fast
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET compareVCF
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET usher
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET matUtils
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET usher-sampled
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET ripplesUtils
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET ripplesInit
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET matOptimize
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET matOptimize
PROTOS mutation_detailed.proto)
protobuf_generate(
LANGUAGE cpp
TARGET usher-sampled
PROTOS mutation_detailed.proto)
protobuf_generate(
LANGUAGE cpp
TARGET output_final_protobuf
PROTOS parsimony.proto)
protobuf_generate(
LANGUAGE cpp
TARGET output_final_protobuf
PROTOS mutation_detailed.proto)
protobuf_generate(
LANGUAGE cpp
TARGET matUtils
PROTOS taxodium.proto)
if(USHER_SERVER)
protobuf_generate(
LANGUAGE cpp
TARGET usher_server
PROTOS parsimony.proto)
endif()
else()
protobuf_generate_cpp(
PROTO_SRCS PROTO_HDRS
parsimony.proto)
protobuf_generate_cpp(
DETAILED_MUTATIONS_PROTO_SRCS
DETAILED_MUTATIONS_PROTO_HDRS
mutation_detailed.proto)
protobuf_generate_cpp(
TAXO_SRCS TAXO_HDRS
taxodium.proto)
add_executable(usher
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/usher_common.cpp
src/usher.cpp
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(matUtils
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${MATUTIL_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
${TAXO_SRCS}
${TAXO_HDRS}
)
add_executable(ripples
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${RIPPLES_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(ripples-fast
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
${RIPPLES_FAST_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(usher-sampled
${USHER_SAMPLED_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
${DETAILED_MUTATIONS_PROTO_SRCS}
${DETAILED_MUTATIONS_PROTO_HDRS}
src/matOptimize/main_helper.cpp
src/matOptimize/detailed_mutations_store.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/reassign_states.cpp
src/matOptimize/check_samples.cpp
src/matOptimize/optimize_tree.cpp
src/matOptimize/condense.cpp
src/matOptimize/Fitch_Sankoff.cpp
src/matOptimize/main_load_tree.cpp
src/matOptimize/priority_conflict_resolver.cpp
src/usher-sampled/driver/main.cpp
${patch_tree}
${New_Profitable_Moves_Enumerators}
)
add_executable(ripplesUtils
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/matUtils/describe.cpp
${RIPPLES_UTILS_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(ripplesInit
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/ripples/init/init_pipeline.cpp
src/ripples/init/main.cpp
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(compareVCF
src/mutation_annotated_tree.cpp
src/compareVCF.cpp
src/usher_mapper.cpp
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(matOptimize
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/detailed_mutations_store.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/main.cpp
src/matOptimize/optimize_tree.cpp
src/matOptimize/import_vcf_fast.cpp
src/matOptimize/condense.cpp
src/matOptimize/VCF_load_tree.cpp
src/matOptimize/main_load_tree.cpp
src/matOptimize/main_helper.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/Fitch_Sankoff.cpp
src/matOptimize/optimize_inner_loop.cpp
src/matOptimize/reassign_states.cpp
src/matOptimize/check_samples.cpp
#src/matOptimize/priority_conflict_resolver_cross_only.cpp
src/matOptimize/priority_conflict_resolver.cpp
src/matOptimize/transpose_vcf/transposed_vcf_patch.cpp
src/usher-sampled/utils.cpp
src/usher-sampled/Min_back_FS.cpp
${patch_tree}
${New_Profitable_Moves_Enumerators}
${PROTO_SRCS}
${PROTO_HDRS}
${DETAILED_MUTATIONS_PROTO_SRCS}
${DETAILED_MUTATIONS_PROTO_HDRS}
)
add_executable(check_samples_place
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/Mutation_Collection.cpp
${check_samples_place}
${PROTO_SRCS}
${PROTO_HDRS}
${DETAILED_MUTATIONS_PROTO_SRCS}
${DETAILED_MUTATIONS_PROTO_HDRS}
)
#[[add_executable(output_final_protobuf
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/main_helper.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/output_final_protobuf.cpp
${PROTO_SRCS}
${PROTO_HDRS}
${DETAILED_MUTATIONS_PROTO_SRCS}
${DETAILED_MUTATIONS_PROTO_HDRS}
)]]
add_executable(transpose_vcf
src/matOptimize/transpose_vcf/transpose_vcf_encode.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
add_executable(transposed_vcf_to_vcf
src/matOptimize/transpose_vcf/transposed_vcf_to_vcf.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
add_executable(transposed_vcf_to_fa
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/transpose_vcf/transposed_vcf_to_fa.cpp
)
add_executable(transposed_vcf_print_name
src/matOptimize/transpose_vcf/transposed_vcf_print_name.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
)
if(USHER_SERVER)
add_executable(usher_server
src/mutation_annotated_tree.cpp
src/usher_mapper.cpp
src/usher_common.cpp
src/usher_server.cpp
${PROTO_SRCS}
${PROTO_HDRS}
)
add_executable(usher-sampled-server
${USHER_SAMPLED_SRCS}
${PROTO_SRCS}
${PROTO_HDRS}
${DETAILED_MUTATIONS_PROTO_SRCS}
${DETAILED_MUTATIONS_PROTO_HDRS}
src/matOptimize/main_helper.cpp
src/matOptimize/detailed_mutations_store.cpp
src/matOptimize/detailed_mutations_load.cpp
src/matOptimize/mutation_annotated_tree.cpp
src/matOptimize/mutation_annotated_tree_node.cpp
src/matOptimize/mutation_annotated_tree_load_store.cpp
src/matOptimize/mutation_annotated_tree_nuc_util.cpp
src/matOptimize/Mutation_Collection.cpp
src/matOptimize/reassign_states.cpp
src/matOptimize/check_samples.cpp
src/matOptimize/optimize_tree.cpp
src/matOptimize/condense.cpp
src/matOptimize/Fitch_Sankoff.cpp
src/matOptimize/main_load_tree.cpp
src/matOptimize/priority_conflict_resolver.cpp
src/usher-sampled/driver/socket.cpp
${patch_tree}
${New_Profitable_Moves_Enumerators}
)
endif()
endif()
if(SAVE_PROFILE)
if(DEBUG)
TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DSAVE_PROFILE=1 -DDEBUG=1)
else(DEBUG)
TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DSAVE_PROFILE=1)
endif(DEBUG)
else(SAVE_PROFILE)
if(DEBUG)
TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DDEBUG=1)
else(DEBUG)
TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
endif(DEBUG)
endif(SAVE_PROFILE)
#set_property(TARGET matOptimize PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
TARGET_LINK_LIBRARIES(compareVCF PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(check_samples_place PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(matOptimize PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(usher-sampled PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
#TARGET_LINK_LIBRARIES(output_final_protobuf PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(transpose_vcf PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(transposed_vcf_to_vcf PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(transposed_vcf_to_fa PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(transposed_vcf_print_name PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(usher PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
target_include_directories(usher PUBLIC "${PROJECT_BINARY_DIR}")
TARGET_COMPILE_OPTIONS(matUtils PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
TARGET_LINK_LIBRARIES(matUtils PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(ripplesUtils PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(ripplesInit PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
TARGET_COMPILE_OPTIONS(ripples PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
TARGET_LINK_LIBRARIES(ripples PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(ripples-fast PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
if(USHER_SERVER)
TARGET_COMPILE_OPTIONS(usher_server PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
TARGET_LINK_LIBRARIES(usher_server PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
TARGET_LINK_LIBRARIES(usher-sampled-server PRIVATE stdc++ ${CMAKE_DL_LIBS} ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
install(TARGETS usher matUtils matOptimize ripples usher_server DESTINATION bin)
else()
install(TARGETS usher matUtils matOptimize ripples DESTINATION bin)
endif()