amber/Makefile at main · genomewalker/amber · GitHub

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
# AMBER - Ancient Metagenomic BinnER
# Makefile
#
# Build with: conda activate assembly && make

CXX := g++
CXXFLAGS := -std=c++17 -O3 -march=native -mtune=native -Wall -Wextra -fopenmp

# Include paths
CXXFLAGS += -Iinclude -Isrc

# Eigen3 detection (for Cholesky decomposition)
ifdef CONDA_PREFIX
EIGEN_CFLAGS ?= -I$(CONDA_PREFIX)/include/eigen3
else
EIGEN_CFLAGS ?= $(shell pkg-config --cflags eigen3 2>/dev/null || echo "-I/usr/include/eigen3")
endif
CXXFLAGS += $(EIGEN_CFLAGS)

# HTSlib detection
# 1. Check CONDA_PREFIX (activated conda env)
# 2. Fall back to pkg-config
# 3. Allow override via HTSLIB_CFLAGS and HTSLIB_LIBS
ifdef CONDA_PREFIX
HTSLIB_CFLAGS ?= -I$(CONDA_PREFIX)/include
HTSLIB_LIBS ?= -L$(CONDA_PREFIX)/lib -lhts -Wl,-rpath,$(CONDA_PREFIX)/lib
else
HTSLIB_CFLAGS ?= $(shell pkg-config --cflags htslib 2>/dev/null || pkg-config --cflags hts 2>/dev/null)
HTSLIB_LIBS ?= $(shell pkg-config --libs htslib 2>/dev/null || pkg-config --libs hts 2>/dev/null || echo "-lhts")
endif
CXXFLAGS += $(HTSLIB_CFLAGS)

LDFLAGS := $(HTSLIB_LIBS) -lz -lpthread -lm

# libleidenalg for exact Leiden clustering (COMEBin matching)
# DISABLED: conda libleidenalg has different API than our patched version
# ifdef CONDA_PREFIX
# ifneq ($(wildcard $(CONDA_PREFIX)/lib/liblibleidenalg.so),)
# CXXFLAGS += -DUSE_LIBLEIDENALG -I$(CONDA_PREFIX)/include -I$(CONDA_PREFIX)/include/libleidenalg
# LDFLAGS += -L$(CONDA_PREFIX)/lib -ligraph -llibleidenalg -Wl,-rpath,$(CONDA_PREFIX)/lib
# $(info Using libleidenalg for exact Leiden clustering)
# endif
# endif

# Directories
SRCDIR := src
ALGDIR := src/algorithms
BINDIR := src/binner
CLIDIR := src/cli

# Target
TARGET := amber

# Debug mode
ifdef DEBUG
CXXFLAGS += -O0 -g -fno-omit-frame-pointer
endif

# Address sanitizer
ifdef ASAN
CXXFLAGS += -fsanitize=address -fno-omit-frame-pointer
LDFLAGS += -fsanitize=address
endif

# Source files
MAIN_SRCS := $(SRCDIR)/main.cpp

CLI_SRCS := \
	$(CLIDIR)/cli_common.cpp \
	$(CLIDIR)/cmd_bin.cpp \
	$(CLIDIR)/cmd_bin2.cpp \
	$(CLIDIR)/cmd_comebin.cpp \
	$(CLIDIR)/cmd_comebin_validate.cpp \
	$(CLIDIR)/cmd_leiden_debug.cpp \
	$(CLIDIR)/cmd_deconvolve.cpp \
	$(CLIDIR)/cmd_embed.cpp \
	$(CLIDIR)/cmd_polish.cpp \
	$(CLIDIR)/cmd_chimera.cpp \
	$(CLIDIR)/cmd_seeds.cpp

MODULE_SRCS := \
	$(SRCDIR)/embed.cpp \
	$(SRCDIR)/polish.cpp \
	$(SRCDIR)/chimera.cpp \
	$(SRCDIR)/bin2.cpp

ALG_SRCS := \
	$(ALGDIR)/fractal_features.cpp \
	$(ALGDIR)/kmer_features.cpp \
	$(ALGDIR)/coverage_features.cpp \
	$(ALGDIR)/damage_features.cpp \
	$(ALGDIR)/damage_profile.cpp \
	$(ALGDIR)/sequence_utils.cpp \
	$(ALGDIR)/pca.cpp \
	$(ALGDIR)/chimera_detector.cpp \
	$(ALGDIR)/ref_reader.cpp \
	$(ALGDIR)/parallel_coverage.cpp

BINNER_SRCS := \
	$(BINDIR)/binner.cpp

BIN2_CLUSTER_SRCS := \
	src/bin2/clustering/hnsw_knn_index.cpp \
	src/bin2/clustering/leiden_backend.cpp \
	src/bin2/clustering/edge_weighter.cpp

SEEDS_SRCS := \
	src/seeds/seed_generator.cpp

COMEBIN_SRCS := \
	src/comebin/comebin_binner.cpp

ALL_SRCS := $(MAIN_SRCS) $(CLI_SRCS) $(MODULE_SRCS) $(ALG_SRCS) $(BINNER_SRCS) $(BIN2_CLUSTER_SRCS) $(SEEDS_SRCS) $(COMEBIN_SRCS)

# Object files
OBJS := $(ALL_SRCS:.cpp=.o)

# Default target
all: $(TARGET)

$(TARGET): $(OBJS)
	$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
	@echo ""
	@echo "Build complete: $(TARGET)"
	@echo "Run './amber --help' to see usage"

# Compile rules
%.o: %.cpp
	$(CXX) $(CXXFLAGS) -c -o $@ $<

# Dependencies (auto-generated would be better, but this works for now)
$(SRCDIR)/main.o: $(SRCDIR)/main.cpp
$(CLIDIR)/cli_common.o: $(CLIDIR)/cli_common.cpp $(CLIDIR)/cli_common.h
$(CLIDIR)/cmd_bin.o: $(CLIDIR)/cmd_bin.cpp $(CLIDIR)/cli_common.h
$(CLIDIR)/cmd_deconvolve.o: $(CLIDIR)/cmd_deconvolve.cpp $(CLIDIR)/cli_common.h
$(CLIDIR)/cmd_embed.o: $(CLIDIR)/cmd_embed.cpp $(CLIDIR)/cli_common.h
$(CLIDIR)/cmd_polish.o: $(CLIDIR)/cmd_polish.cpp $(CLIDIR)/cli_common.h
$(CLIDIR)/cmd_chimera.o: $(CLIDIR)/cmd_chimera.cpp $(CLIDIR)/cli_common.h
$(SRCDIR)/embed.o: $(SRCDIR)/embed.cpp
$(SRCDIR)/polish.o: $(SRCDIR)/polish.cpp
$(SRCDIR)/chimera.o: $(SRCDIR)/chimera.cpp
$(BINDIR)/binner.o: $(BINDIR)/binner.cpp

clean:
	rm -f $(TARGET) $(OBJS)
	@echo "Cleaned build artifacts"

# Install target
PREFIX ?= /usr/local
install: $(TARGET)
	install -d $(PREFIX)/bin
	install -m 755 $(TARGET) $(PREFIX)/bin/

.PHONY: all clean install