De-duplicate makefiles

 - the make files are identical after removing redundant declarations
 - use an include to import the common declarations
 - any subsequent overrides to the common declarations can be
   made in the module-specific makefiles below the include statement
 - this eliminates maintenance of around 600 lines of duplicate code
   without compromise in functionality

Signed-off-by: Sven-Thorsten Dietrich <[email protected]>

common/makefile

@@ -0,0 +1,136 @@
+#COMPILER MODE C++17
+CXX=g++ -std=c++17
+
+
+#create folders
+dummy_build_folder_bin := $(shell mkdir -p bin)
+dummy_build_folder_obj := $(shell mkdir -p obj)
+
+#COMPILER & LINKER FLAGS
+CXXFLAG=-O3 -mavx2 -mfma
+LDFLAG=-O3
+
+#COMMIT TRACING
+COMMIT_VERS=$(shell git rev-parse --short HEAD)
+COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
+CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
+CXXFLAG+= -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
+
+#DYNAMIC LIBRARIES
+DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto
+
+HFILE=$(shell find src -name *.h)
+CFILE=$(shell find src -name *.cpp)
+OFILE=$(shell for file in `find src -name *.cpp`; do echo obj/$$(basename $$file .cpp).o; done)
+VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
+
+NAME=$(shell basename $(CURDIR))
+BFILE=bin/$(NAME)
+EXEFILE=bin/$(NAME)_static
+
+#CONDITIONAL PATH DEFINITONS
+system: DYN_LIBS=-lz -lpthread -lbz2 -llzma
+system: HTSSRC=/usr/local
+system: HTSLIB_INC=$(HTSSRC)/include/htslib
+system: HTSLIB_LIB=$(HTSSRC)/lib/libhts.a
+system: BOOST_INC=/usr/include
+system: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+system: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+system: BOOST_LIB_SE=/usr/lib/x86_64-linux-gnu/libboost_serialization.a
+system: $(BFILE)
+
+desktop: HTSSRC=../..
+desktop: HTSLIB_INC=$(HTSSRC)/htslib
+desktop: HTSLIB_LIB=$(HTSSRC)/htslib/libhts.a
+desktop: BOOST_INC=/usr/include
+desktop: BOOST_LIB_IO=/usr/local/lib/libboost_iostreams.a
+desktop: BOOST_LIB_PO=/usr/local/lib/libboost_program_options.a
+desktop: $(BFILE)
+
+olivier: HTSSRC=$(HOME)/Tools
+olivier: HTSLIB_INC=$(HTSSRC)/htslib-1.15
+olivier: HTSLIB_LIB=$(HTSSRC)/htslib-1.15/libhts.a
+olivier: BOOST_INC=/usr/include
+olivier: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+olivier: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+olivier: $(BFILE)
+
+laptop: HTSSRC=$(HOME)/Tools
+laptop: HTSLIB_INC=$(HTSSRC)/htslib-1.10
+laptop: HTSLIB_LIB=$(HTSSRC)/htslib-1.10/libhts.a
+laptop: BOOST_INC=/usr/include
+laptop: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+laptop: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+laptop: $(BFILE)
+
+debug: CXXFLAG=-g -mavx2 -mfma
+debug: LDFLAG=-g
+debug: HTSSRC=$(HOME)/Tools
+debug: HTSLIB_INC=$(HTSSRC)/htslib-1.15
+debug: HTSLIB_LIB=$(HTSSRC)/htslib-1.15/libhts.a
+debug: BOOST_INC=/usr/include
+debug: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+debug: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+debug: $(BFILE)
+
+curnagl: DYN_LIBS=-lz -lpthread -lcrypto /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/xz-5.2.5-3zvzfm67t6ebuerybemshylrysbphghz/lib/liblzma.so /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/bzip2-1.0.8-tsmb67uwhlqn5g6h6etjvftugq7y6mtl/lib/libbz2.so /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/curl-7.74.0-fcqjhj645xhqp2ilrzafwqtqqnu7g42v/lib/libcurl.so
+curnagl: HTSSRC=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/htslib-1.12-p4n5q4icj4g5e4of7mxq2i5xly4v4tax
+curnagl: HTSLIB_INC=$(HTSSRC)/include
+curnagl: HTSLIB_LIB=$(HTSSRC)/lib/libhts.a
+curnagl: BOOST_INC=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/include
+curnagl: BOOST_LIB_IO=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/lib/libboost_iostreams.a
+curnagl: BOOST_LIB_PO=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/lib/libboost_program_options.a
+curnagl: $(BFILE)
+
+jura: HTSSRC=/scratch/beegfs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/htslib-1.12
+jura: HTSLIB_INC=$(HTSSRC)
+jura: HTSLIB_LIB=$(HTSSRC)/libhts.a
+jura: BOOST_INC=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/include
+jura: BOOST_LIB_IO=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/lib/libboost_iostreams.a
+jura: BOOST_LIB_PO=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/lib/libboost_program_options.a
+jura: $(BFILE)
+
+wally: HTSSRC=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/htslib_v1.12
+wally: HTSLIB_INC=$(HTSSRC)
+wally: HTSLIB_LIB=$(HTSSRC)/libhts.a
+wally: BOOST_INC=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/include
+wally: BOOST_LIB_IO=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/lib/libboost_iostreams.a
+wally: BOOST_LIB_PO=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/lib/libboost_program_options.a
+wally: $(BFILE)
+
+static_exe: CXXFLAG=-O2 -mavx2 -mfma -D__COMMIT_ID__=\"$(COMMIT_VERS)\" -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
+static_exe: LDFLAG=-O2
+static_exe: HTSSRC=../..
+static_exe: HTSLIB_INC=$(HTSSRC)/htslib_minimal
+static_exe: HTSLIB_LIB=$(HTSSRC)/htslib_minimal/libhts.a
+static_exe: BOOST_INC=/usr/include
+static_exe: BOOST_LIB_IO=/usr/local/lib/libboost_iostreams.a
+static_exe: BOOST_LIB_PO=/usr/local/lib/libboost_program_options.a
+static_exe: $(EXEFILE)
+
+# static desktop Robin
+static_exe_robin_desktop: CXXFLAG=-O2 -mavx2 -mfma -D__COMMIT_ID__=\"$(COMMIT_VERS)\" -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
+static_exe_robin_desktop: LDFLAG=-O2
+static_exe_robin_desktop: HTSSRC=/home/robin/Dropbox/LIB
+static_exe_robin_desktop: HTSLIB_INC=$(HTSSRC)/htslib_minimal
+static_exe_robin_desktop: HTSLIB_LIB=$(HTSSRC)/htslib_minimal/libhts.a
+static_exe_robin_desktop: BOOST_INC=/usr/include
+static_exe_robin_desktop: BOOST_LIB_IO=$(HTSSRC)/boost/lib/libboost_iostreams.a
+static_exe_robin_desktop: BOOST_LIB_PO=$(HTSSRC)/boost/lib/libboost_program_options.a
+static_exe_robin_desktop: $(EXEFILE)
+
+
+#COMPILATION RULES
+all: desktop
+
+$(BFILE): $(OFILE)
+	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -o $@ $(DYN_LIBS)
+
+$(EXEFILE): $(OFILE)
+	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -Wl,-Bstatic $(DYN_LIBS)
+
+obj/%.o: %.cpp $(HFILE)
+	$(CXX) $(CXXFLAG) -c $< -o $@ -Isrc -I$(HTSLIB_INC) -I$(BOOST_INC)
+
+clean: 
+	rm -f obj/*.o $(BFILE) $(EXEFILE)

ligate/makefile

@@ -1 +1 @@
--include ../common/makefile_common.mk
+include ../common/makefile

phase_common/makefile

@@ -1 +1 @@
-include ../common/makefile_common.mk
+include ../common/makefile

phase_rare/makefile

@@ -1 +1 @@
-include ../common/makefile_common.mk
+include ../common/makefile

simulate/makefile

@@ -1 +1 @@
-include ../common/makefile_common.mk
+include ../common/makefile

switch/makefile

@@ -1 +1 @@
--include ../common/makefile_common.mk
+include ../common/makefile