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#
# VARIABLES
#
VERSION = 1.3.0
#
# PATHS
#
SRC_DIR = src
CPP_DIR = $(shell realpath -e $(SRC_DIR)/cpp)
SCRIPTS_DIR = $(SRC_DIR)/scripts
WEB_DIR = $(SRC_DIR)/web
BUILD_DIR = build
TEST_DIR = testing
SRC_CPP := $(wildcard $(CPP_DIR)/*.cpp)
SRC_HPP := $(wildcard $(CPP_DIR)/*.hpp)
INCLUDES := $(addprefix -I,$(CPP_DIR))
SCRIPTS := $(wildcard $(SCRIPTS_DIR)/*)
# where to install -- the default location assumes environment modules
# are in use, but you can simply override prefix with a command like
# 'make install prefix=...'
MODULES_ROOT = /lab/sw/modules
prefix = $(MODULES_ROOT)/ataqv/$(VERSION)
# where to install the modulefile
MODULEFILES_ROOT = /lab/sw/modulefiles
MODULEFILE_PATH = $(MODULEFILES_ROOT)/ataqv/$(VERSION)
#
# FLAGS
#
CPPFLAGS += -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC $(INCLUDES)
CXXFLAGS += -std=c++11 -pthread -O3 -g $(CPPFLAGS)
CXXFLAGS_DEV = $(CXXFLAGS) # -std=c++11 -pthread -O3 -g $(CPPFLAGS)
CXXFLAGS_STATIC = -std=c++11 -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -static -static-libgcc -static-libstdc++ -I$(HTSLIB_STATIC_DIR) $(CPPFLAGS)
#
# Try to locate dependencies using environment variables
#
#
# Boost
#
#
# If your Boost installation used their 'tagged' layout, the libraries
# will include metadata in their names. Specify BOOST_TAGGED=yes in
# your make command to link with tagged libraries.
#
ifdef BOOST_TAGGED
BOOST_LIBS = -lboost_filesystem-mt -lboost_iostreams-mt -lboost_system-mt -lboost_chrono-mt
else
BOOST_LIBS = -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono
endif
ifdef BOOST_ROOT
CPPFLAGS += -I$(BOOST_ROOT)/include
LDFLAGS += -L$(BOOST_ROOT)/lib
else
ifdef BOOST_INCLUDE
CPPFLAGS += -I$(BOOST_INCLUDE
endif
ifdef BOOST_LIB
LDFLAGS += -L$(BOOST_LIB)
endif
endif
#
# HTSlib
#
ifdef HTSLIB_ROOT
CPPFLAGS += -I$(HTSLIB_ROOT)/include
LDFLAGS += -L$(HTSLIB_ROOT)/lib
else
ifdef HTSLIB_INCLUDE
CPPFLAGS += -I$(HTSLIB_INCLUDE)
endif
ifdef HTSLIB_LIB
LDFLAGS += -L$(HTSLIB_LIB)
endif
endif
#
# htslib can be built with cURL to support HTTPS, which is cool, but
# drags in more libraries
#
ifdef HTSLIBCURL
HTS_LIBS = -lhts -lssl -lcurl -lcrypto
else
HTS_LIBS = -lhts
endif
LDLIBS = $(BOOST_LIBS) $(HTS_LIBS) -lz -lncurses -lpthread
HTSLIB_STATIC_DIR = $(HOME)/sw/bio/htslib/htslib
LDLIBS_STATIC = -L$(HTSLIB_STATIC_DIR) $(LDLIBS) -lbz2 -llzma -ltinfo -lrt
#
# Architecture flags
#
UNAME_P := $(shell uname -p)
ifeq ($(UNAME_P),x86_64)
CPPFLAGS += -D AMD64
endif
ifneq ($(filter %86,$(UNAME_P)),)
CPPFLAGS += -D IA32
endif
ifneq ($(filter arm%,$(UNAME_P)),)
CPPFLAGS += -D ARM
endif
UNAME_S := $(shell uname -s)
ifeq ($(UNAME_S),Linux)
CPPFLAGS += -D LINUX
endif
#
# TARGETS
#
.PHONY: all checkdirs clean deb deb-static rpm install install-ataqv install-module install-scripts install-web test
all: checkdirs $(BUILD_DIR)/ataqv
static: checkdirs $(BUILD_DIR)/ataqv-static
dist: checkdirs $(BUILD_DIR)/ataqv
make install DESTDIR=$(BUILD_DIR)/ataqv-$(VERSION) prefix=
cd $(BUILD_DIR) && tar czf ataqv-$(VERSION).$(shell uname -m).$(shell uname -s).tar.gz ataqv-$(VERSION)
dist-static: checkdirs $(BUILD_DIR)/ataqv-static
make install DESTDIR=$(BUILD_DIR)/ataqv-$(VERSION) prefix=
install -m 0755 $(BUILD_DIR)/ataqv-static $(BUILD_DIR)/ataqv-$(VERSION)/bin/ataqv
cd $(BUILD_DIR) && tar czf ataqv-$(VERSION).$(shell uname -m).$(shell uname -s).tar.gz ataqv-$(VERSION)
deb:
(cd .. && tar czf ataqv_$(VERSION).orig.tar.gz --exclude .git --exclude build ataqv)
debuild -uc -us -d
deb-static: deb static
install -m 0755 $(BUILD_DIR)/ataqv-static debian/ataqv/usr/bin/ataqv
sed -i '/Depends: /d' debian/ataqv/DEBIAN/control
dh_builddeb
rpm: deb
(cd .. && alien -r ataqv_$(VERSION)-1_amd64.deb)
rpm-static: deb-static
(cd .. && alien -r ataqv_$(VERSION)-1_amd64.deb)
checkdirs: $(BUILD_DIR) $(TEST_DIR)
$(BUILD_DIR):
@mkdir -p $@
$(TEST_DIR):
@mkdir -p $@
$(BUILD_DIR)/ataqv: $(BUILD_DIR)/ataqv.o $(BUILD_DIR)/Features.o $(BUILD_DIR)/HTS.o $(BUILD_DIR)/IO.o $(BUILD_DIR)/Metrics.o $(BUILD_DIR)/Peaks.o $(BUILD_DIR)/Utils.o
$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
$(BUILD_DIR)/ataqv-static: $(CPP_DIR)/ataqv.cpp $(CPP_DIR)/Features.cpp $(CPP_DIR)/HTS.cpp $(CPP_DIR)/IO.cpp $(CPP_DIR)/Metrics.cpp $(CPP_DIR)/Peaks.cpp $(CPP_DIR)/Utils.cpp
$(CXX) -o $@ $^ $(CXXFLAGS_STATIC) $(LDFLAGS) $(LDLIBS_STATIC)
$(BUILD_DIR)/%.o: $(CPP_DIR)/%.cpp $(SRC_HPP) $(CPP_DIR)/Version.hpp
$(CXX) $(CXXFLAGS) -o $@ -c $<
$(CPP_DIR)/Version.hpp: Makefile
@echo '//' >$@
@echo '// Copyright 2015 Stephen Parker' >>$@
@echo '//' >>$@
@echo '// Licensed under Version 3 of the GPL or any later version' >>$@
@echo '//' >>$@
@echo >>$@
@echo '#define VERSION "$(VERSION)"' >>$@
test: checkdirs $(CPP_DIR)/Version.hpp $(TEST_DIR)/run_ataqv_tests
@cp testdata/* $(TEST_DIR)
@cd $(TEST_DIR) && ./run_ataqv_tests -i
$(TEST_DIR)/run_ataqv_tests: $(TEST_DIR)/run_ataqv_tests.o $(TEST_DIR)/test_features.o $(TEST_DIR)/test_hts.o $(TEST_DIR)/test_io.o $(TEST_DIR)/test_metrics.o $(TEST_DIR)/test_peaks.o $(TEST_DIR)/test_utils.o $(TEST_DIR)/Features.o $(TEST_DIR)/HTS.o $(TEST_DIR)/IO.o $(TEST_DIR)/Metrics.o $(TEST_DIR)/Peaks.o $(TEST_DIR)/Utils.o
$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) $(LDLIBS)
$(TEST_DIR)/%.o: $(CPP_DIR)/%.cpp $(SRC_HPP)
$(CXX) $(CXXFLAGS_DEV) -o $@ -c $<
clean:
@rm -rf $(BUILD_DIR) $(TEST_DIR)
@test -x dh_clean && dh_clean || true
install: checkdirs install-ataqv install-scripts install-web
install-ataqv: $(BUILD_DIR)/ataqv
@echo "Installing to $(prefix)"
install -d -m 0755 $(DESTDIR)$(prefix)/bin
install -m 0755 build/ataqv $(DESTDIR)$(prefix)/bin
install-scripts: $(SCRIPTS)
install -d -m 0755 $(DESTDIR)$(prefix)/bin
for f in $^; do sed -e 's/{{VERSION}}/$(VERSION)/g' $$f > $(BUILD_DIR)/$$(basename $$f); install -m 0755 $(BUILD_DIR)/$$(basename $$f) $(DESTDIR)$(prefix)/bin; done
install-web: $(WEB_DIR)
install -d -m 0755 $(DESTDIR)$(prefix)/share/ataqv/web
cp -a $^/* $(DESTDIR)$(prefix)/share/ataqv/web
find $(DESTDIR)$(prefix)/share/ataqv/web -type d -exec chmod 755 {} \;
find $(DESTDIR)$(prefix)/share/ataqv/web -type f -exec chmod 644 {} \;
ifdef MODULEFILE_PATH
# template for environment module file
define MODULEFILE
#%Module1.0
set version $(VERSION)
set app ataqv
set modroot $(MODULES_ROOT)/$$app/$$version
setenv ATAQV_MODULE $$modroot
prepend-path PATH $$modroot/bin
conflict ataqv
module-whatis "ATAC-seq QC toolkit, version $$version."
module-whatis "URL: https://github.com/ParkerLab/ataqv"
module-whatis "Installation directory: $$modroot"
endef
export MODULEFILE
install-module: install
mkdir -p `dirname $(DESTDIR)$(MODULEFILE_PATH)`
echo "$$MODULEFILE" > $(DESTDIR)$(MODULEFILE_PATH)
endif
|
