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|
# ==========================
# Lumpy Makefile
# (c) 2016 Jim Havrilla
# ==========================
SHELL := /bin/bash -e
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
# define our object and binary directories
export OBJ_DIR = obj
export BIN_DIR = bin
export SRC_DIR = src
export UTIL_DIR = src/utils
export SCRIPTS_DIR = scripts
export CXX = g++
ifeq ($(ZLIB_PATH),)
export ZLIB_PATH=$(HOME)/src/zlib-1.2.8
endif
#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -DTRACE
#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC
export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
export LIBS = -lz -L $(ZLIB_PATH)
#export BT_ROOT = src/utils/BamTools/
export MKFILE_DIR = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
SUBDIRS = $(SRC_DIR)/lumpy
UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
$(SRC_DIR)/utils/version \
$(SRC_DIR)/utils/fileType \
$(SRC_DIR)/utils/bedFilePE \
$(SRC_DIR)/utils/genomeFile \
$(SRC_DIR)/utils/BamTools-Ancillary \
$(SRC_DIR)/utils/sequenceUtilities \
all: lumpy_filter lumpyexpress lumpy
lumpy:
[ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
@echo "Building lumpy:"
@echo "========================================================="
#$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
for dir in $(UTIL_SUBDIRS); do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $$dir; \
echo ""; \
done
@for dir in $(SUBDIRS); do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $$dir; \
echo ""; \
done
lumpy_filter: # htslib - use Debian packaged htslib
[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
$(MAKE) --no-print-directory -C src/filter/
cp src/filter/lumpy_filter $(BIN_DIR)
htslib:
$(shell cd lib/htslib && autoreconf)
cd lib/htslib && \
./configure --disable-bz2 --disable-lzma --enable-libcurl
CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT"
lumpyexpress:
[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
cp $(SCRIPTS_DIR)/lumpyexpress $(BIN_DIR)/lumpyexpress
> $(BIN_DIR)/lumpyexpress.config
@echo "LUMPY_HOME=$(MKFILE_DIR)" >> $(BIN_DIR)/lumpyexpress.config
@echo "" >> $(BIN_DIR)/lumpyexpress.config
@echo "LUMPY=$(MKFILE_DIR)/$(BIN_DIR)/lumpy" >> $(BIN_DIR)/lumpyexpress.config
@echo "HEXDUMP=`which hexdump`" >> $(BIN_DIR)/lumpyexpress.config
@echo "SAMBLASTER=`which samblaster`" >> $(BIN_DIR)/lumpyexpress.config
@echo "SAMBAMBA=`which sambamba`" >> $(BIN_DIR)/lumpyexpress.config
@echo "SAMTOOLS=`which samtools`" >> $(BIN_DIR)/lumpyexpress.config
@echo "PYTHON=`which python`" >> $(BIN_DIR)/lumpyexpress.config
@echo "" >> $(BIN_DIR)/lumpyexpress.config
@echo "PAIREND_DISTRO=$(MKFILE_DIR)/$(SCRIPTS_DIR)/pairend_distro.py" >> $(BIN_DIR)/lumpyexpress.config
@echo "BAMGROUPREADS=$(MKFILE_DIR)/$(SCRIPTS_DIR)/bamkit/bamgroupreads.py" >> $(BIN_DIR)/lumpyexpress.config
@echo "BAMFILTERRG=$(MKFILE_DIR)/$(SCRIPTS_DIR)/bamkit/bamfilterrg.py" >> $(BIN_DIR)/lumpyexpress.config
@echo "BAMLIBS=$(MKFILE_DIR)/$(SCRIPTS_DIR)/bamkit/bamlibs.py" >> $(BIN_DIR)/lumpyexpress.config
.PHONY: all
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
#rm -Rf $(BT_ROOT)/lib
#rm -f $(BT_ROOT)/src/api/*.o
#rm -f $(BT_ROOT)/src/api/internal/*.o
#rm -Rf $(BT_ROOT)/include
.PHONY: clean
|
