/
Makefile
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/
Makefile
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# Pheniqs : PHilology ENcoder wIth Quality Statistics
# Copyright (C) 2017 Lior Galanti
# NYU Center for Genetics and System Biology
# Author: Lior Galanti <lior.galanti@nyu.edu>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
MAJOR_REVISON := 1
MINOR_REVISON := 0
-include environment.mk
# Construct version variable
GIT_VERSION := $(shell git describe --abbrev=40 --always 2> /dev/null)
ifdef GIT_VERSION
PACKAGE_VERSION := $(MAJOR_REVISON).$(MINOR_REVISON).$(GIT_VERSION)
else
PACKAGE_VERSION := $(MAJOR_REVISON).$(MINOR_REVISON)
endif
LIBS = -lhts -lz
CC = clang++
CFLAGS = -c -std=c++11 -O3 -Wall -Wsign-compare
LDFLAGS = $(LIBS)
SOURCES = \
constant.cpp \
model.cpp \
feed.cpp \
environment.cpp \
pipeline.cpp \
pheniqs.cpp
OBJECTS = \
constant.o \
model.o \
feed.o \
environment.o \
pipeline.o \
pheniqs.o
EXECUTABLE = pheniqs
# OS detection
# PLATFORM := $(shell uname -s)
# ifeq ($(PLATFORM),Linux)
# # CFLAGS +=
# endif
# ifeq ($(PLATFORM),Darwin)
# # CFLAGS += -stdlib=libc++
# endif
ifdef HTSLIB
CFLAGS += -I$(HTSLIB)/include
LDFLAGS += -L$(HTSLIB)/lib
endif
ifdef RAPIDJSON
CFLAGS += -I$(RAPIDJSON)/include
endif
all: $(SOURCES) configuration.h version.h $(EXECUTABLE)
.cpp.o:
$(CC) $(CFLAGS) -c -o $@ $<
$(EXECUTABLE): $(OBJECTS)
$(CC) $(OBJECTS) -o $@ $(LDFLAGS)
# Regenerate version.h when PACKAGE_VERSION changes
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,clean-version))
@echo Generate version.h with $(PACKAGE_VERSION)
@echo '#define PHENIQS_VERSION "$(PACKAGE_VERSION)"' > $@
# Regenerate configuration.h when interface.json file changes
configuration.h: interface.json
@echo Generate command line interface configuration
@xxd -i interface.json > $@
clean-version:
-@rm -f version.h
clean-configuration:
-@rm -f configuration.h
clean: clean-version clean-configuration
-@rm -f $(EXECUTABLE) $(OBJECTS)
# Dependencies
# Regenerate modules when header files they import change
constant.o: \
constant.h
model.o: \
constant.h \
error.h \
model.h
feed.o: \
constant.h \
error.h \
model.h \
feed.h
environment.o: \
constant.h \
error.h \
model.h \
feed.h \
interface.h \
configuration.h \
version.h \
environment.h
pipeline.o: \
feed.h \
environment.h \
pipeline.h
pheniqs.o: \
constant.h \
pipeline.h