forked from refresh-bio/SPLASH
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Makefile
223 lines (178 loc) · 5.19 KB
/
Makefile
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
all: satc satc_dump satc_merge sig_anch compactors download_kmc splash supervised_test dsv_manip
dummy := $(shell git submodule update --init --recursive)
SPLASH_LIBS_DIR = libs
LIBS_DIR = . #/usr/local/lib
INCLUDE_DIR= libs
ZLIB_INCLUDE_DIR= libs/cloudflare-zlib
SATC_MAIN_DIR=src/satc
SATC_MERGE_MAIN_DIR=src/satc_merge
SATC_DUMP_MAIN_DIR=src/satc_dump
SIG_ANCH_MAIN_DIR=src/sig_anch
DSV_MANIP_MAIN_DIR=src/dsv_manip
COMMON_DIR=src/common
COMPACTORS_MAIN_DIR=src/compactors
OUT_BIN_DIR=bin
ifdef MSVC # Avoid the MingW/Cygwin sections
UNAME_S := Windows
else # If uname not available => 'not'
UNAME_S := $(shell sh -c 'uname -s 2>/dev/null || echo not')
UNAME_M := $(shell uname -m)
endif
D_OS =
D_ARCH =
ifeq ($(UNAME_S),Darwin)
D_OS=MACOS
ifeq ($(UNAME_M),arm64)
D_ARCH=ARM64
else
D_ARCH=X64
endif
else
D_OS=LINUX
D_ARCH=X64
ifeq ($(UNAME_M),arm64)
D_ARCH=ARM64
endif
ifeq ($(UNAME_M),aarch64)
D_ARCH=ARM64
endif
endif
CPU_FLAGS =
STATIC_LFLAGS =
PLATFORM_SPECIFIC_FLAGS =
#in some cases we can have different results on ARM
#I guess this is exactly the same as here: https://bugs.mysql.com/bug.php?id=82760
ifeq ($(D_ARCH),ARM64)
PLATFORM_SPECIFIC_FLAGS = -ffp-contract=off
endif
ifeq ($(D_OS),MACOS)
CC = g++-11
ifeq ($(D_ARCH),ARM64)
CPU_FLAGS = -march=armv8.4-a
else
CPU_FLAGS = -m64
endif
STATIC_LFLAGS = -static-libgcc -static-libstdc++ -pthread
else
CC = g++
ifeq ($(D_ARCH),ARM64)
CPU_FLAGS = -march=armv8-a
STATIC_LFLAGS = -static-libgcc -static-libstdc++ -lpthread
else
CPU_FLAGS = -m64
STATIC_LFLAGS = -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
endif
endif
CFLAGS = -fPIC -Wall -O3 $(PLATFORM_SPECIFIC_FLAGS) $(CPU_FLAGS) -std=c++17 -pthread -I $(INCLUDE_DIR) -I $(ZLIB_INCLUDE_DIR) -fpermissive
CLINK = -lm -std=c++17 -lpthread
release: CLINK = -lm -std=c++17 $(STATIC_LFLAGS)
release: CLINK = -lm -std=c++17 $(STATIC_LFLAGS)
release: CFLAGS = -fPIC -Wall -O3 -DNDEBUG $(PLATFORM_SPECIFIC_FLAGS) $(CPU_FLAGS) -std=c++17 -pthread -I $(INCLUDE_DIR) -I $(ZLIB_INCLUDE_DIR) -fpermissive
release: all
debug: CFLAGS = -fPIC -Wall -O0 -g $(PLATFORM_SPECIFIC_FLAGS) $(CPU_FLAGS) -std=c++17 -pthread -I $(INCLUDE_DIR) -I $(ZLIB_INCLUDE_DIR) -fpermissive
debug: all
ifeq ($(UNAME_S),Linux)
CLINK+=-fabi-version=6
endif
LIB_ZLIB=$(SPLASH_LIBS_DIR)/cloudflare-zlib/libz.a
LIB_ZSTD=$(SPLASH_LIBS_DIR)/zstd/lib/libzstd.a
# default install location (binary placed in the /bin folder)
ifeq ($(PREFIX),)
PREFIX ?= /usr/local
endif
$(LIB_ZLIB):
cd $(SPLASH_LIBS_DIR)/cloudflare-zlib; ./configure; make libz.a
$(LIB_ZSTD):
cd $(SPLASH_LIBS_DIR)/zstd; make -j
%.o: %.cpp
$(CC) $(CFLAGS) -c $< -o $@
satc: $(OUT_BIN_DIR)/satc
$(OUT_BIN_DIR)/satc: $(SATC_MAIN_DIR)/satc.o \
$(COMMON_DIR)/kmc_api/kmc_file.o \
$(COMMON_DIR)/kmc_api/mmer.o \
$(COMMON_DIR)/kmc_api/kmer_api.o \
$(COMMON_DIR)/illumina_adapters_static.o \
$(LIB_ZSTD)
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(LIB_ZSTD) \
$(CLINK)
satc_merge: $(OUT_BIN_DIR)/satc_merge
$(OUT_BIN_DIR)/satc_merge: $(SATC_MERGE_MAIN_DIR)/satc_merge.o \
$(SATC_MERGE_MAIN_DIR)/pvals.o \
$(SATC_MERGE_MAIN_DIR)/anchor.o \
$(SATC_MERGE_MAIN_DIR)/extra_stats.o \
$(LIB_ZSTD)
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(LIB_ZSTD) \
$(CLINK)
satc_dump: $(OUT_BIN_DIR)/satc_dump
$(OUT_BIN_DIR)/satc_dump: $(SATC_DUMP_MAIN_DIR)/satc_dump.o $(LIB_ZSTD)
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(LIB_ZSTD) \
$(CLINK)
sig_anch: $(OUT_BIN_DIR)/sig_anch
$(OUT_BIN_DIR)/sig_anch: $(SIG_ANCH_MAIN_DIR)/sig_anch.o \
$(COMMON_DIR)/csv.o
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(CLINK)
compactors: $(OUT_BIN_DIR)/compactors
$(OUT_BIN_DIR)/compactors: $(COMPACTORS_MAIN_DIR)/main.o \
$(COMPACTORS_MAIN_DIR)/console.o \
$(COMPACTORS_MAIN_DIR)/engine.o \
$(COMPACTORS_MAIN_DIR)/io.o \
$(COMPACTORS_MAIN_DIR)/main.o \
$(COMPACTORS_MAIN_DIR)/read_select.o \
$(COMMON_DIR)/edit_distance.o \
$(COMMON_DIR)/illumina_adapters_static.o \
$(LIB_ZLIB) \
$(SPLASH_LIBS_DIR)/cdflib/cdflib.o
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(LIB_ZLIB) \
$(CLINK)
dsv_manip: $(OUT_BIN_DIR)/dsv_manip
$(OUT_BIN_DIR)/dsv_manip: $(DSV_MANIP_MAIN_DIR)/dsv_manip.o \
$(DSV_MANIP_MAIN_DIR)/dsv_common.o \
$(DSV_MANIP_MAIN_DIR)/limit_mode.o \
$(DSV_MANIP_MAIN_DIR)/sort_mode.o
-mkdir -p $(OUT_BIN_DIR)
$(CC) -o $@ $^ \
$(CLINK)
download_kmc:
-mkdir -p $(OUT_BIN_DIR)
./download_kmc.py $(OUT_BIN_DIR)
splash:
-mkdir -p $(OUT_BIN_DIR)
cp src/splash.py bin/splash
supervised_test:
-mkdir -p $(OUT_BIN_DIR)
cp src/supervised_test/supervised_test.R bin
install: all
install -d $(PREFIX)/bin
install bin/* $(PREFIX)/bin
uninstall:
-rm $(PREFIX)/bin/satc
-rm $(PREFIX)/bin/compactors
-rm $(PREFIX)/bin/satc_dump
-rm $(PREFIX)/bin/satc_merge
-rm $(PREFIX)/bin/sig_anch
-rm $(PREFIX)/bin/splash
-rm $(PREFIX)/bin/kmc
-rm $(PREFIX)/bin/kmc_tools
-rm $(PREFIX)/bin/dsv_manip
-rm $(PREFIX)/bin/supervised_test.R
clean:
-rm $(SATC_MAIN_DIR)/*.o
-rm $(COMMON_DIR)/kmc_api/*.o
-rm $(SATC_MERGE_MAIN_DIR)/*.o
-rm $(SATC_DUMP_MAIN_DIR)/*.o
-rm $(COMPACTORS_MAIN_DIR)/*.o
-rm $(COMMON_DIR)/*.o
-rm $(SIG_ANCH_MAIN_DIR)/*.o
-rm $(DSV_MANIP_MAIN_DIR)/*.o
-rm -rf $(OUT_BIN_DIR)
-rm $(SPLASH_LIBS_DIR)/cdflib/*.o