Makefile: Clean, search for libraries, dynamic/static compilation

Compile with the static .a libraries only when compiling the static
exe. Search for the .a static libraries in system automatically and
warn if they are not found. Clean the rules to use the library
paths found. Add dynamic libraries for boost and htslib when
linking the normal exe (the non static one).

Signed-off-by: Rick Wertenbroek <[email protected]>

common/makefile_common.mk

@@ -16,8 +16,10 @@ 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
+# DYNAMIC LIBRARIES # Standard libraries are still dynamic in static exe
+DYN_LIBS_FOR_STATIC=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+# Non static exe links with all libraries
+DYN_LIBS=$(DYN_LIBS_FOR_STATIC) -lboost_iostreams -lboost_program_options -lboost_serialization -lhts
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -28,22 +30,65 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/$(NAME)
 EXEFILE=bin/$(NAME)_static
 
+# Only search for libraries if goals != clean
+ifeq (,$(filter clean,$(MAKECMDGOALS)))
+
+#################################
+# HTSLIB for static compilation #
+#################################
+# These are the default paths when installing htslib from source
+HTSSRC=/usr/local
+HTSLIB_INC=$(HTSSRC)/include/htslib
+HTSLIB_LIB=$(HTSSRC)/lib/libhts.a
+
+##########################################
+# Boost libraries for static compilation #
+##########################################
+BOOST_INC=/usr/include
+
+# If not set by user command, search for it
+BOOST_LIB_IO?=$(shell whereis libboost_iostreams | grep -o '\S*\.a\b')
+ifneq ($(suffix $(BOOST_LIB_IO)),.a)
+    # If not found check default path
+    ifeq ($(wildcard /usr/local/lib/libboost_iostreams.a),)
+        # File does not exist
+        $(warning libboost_iostreams.a not found, you can specify it with "make BOOST_LIB_IO=/path/to/lib...")
+    else
+        # File exists, set the variable
+        BOOST_LIB_IO=/usr/local/lib/libboost_iostreams.a
+    endif
+endif
+
+# If not set by user command, search for it
+BOOST_LIB_PO?=$(shell whereis libboost_program_options | grep -o '\S*\.a\b')
+ifneq ($(suffix $(BOOST_LIB_PO)),.a)
+    # If not found check default path
+    ifeq ($(wildcard /usr/local/lib/libboost_program_options.a),)
+        # File does not exist
+        $(warning libboost_program_options.a not found, you can specify it with "make BOOST_LIB_PO=/path/to/lib...")
+    else
+        # File exists, set the variable
+        BOOST_LIB_PO=/usr/local/lib/libboost_program_options.a
+    endif
+endif
+
+# If not set by user command, search for it
+BOOST_LIB_SE?=$(shell whereis libboost_serialization | grep -o '\S*\.a\b')
+ifneq ($(suffix $(BOOST_LIB_SE)),.a)
+    # If not found check default path
+    ifeq ($(wildcard /usr/local/lib/libboost_serialization.a),)
+        # File does not exist
+        $(warning libboost_serialization.a not found, you can specify it with "make BOOST_LIB_SE=/path/to/lib...")
+    else
+        # File exists, set the variable
+        BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
+    endif
+endif
+
+# Endif makefile goals != clean
+endif
+
 #CONDITIONAL PATH DEFINITON
-system: HTSSRC=/usr/local
-system: HTSLIB_INC=$(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
@@ -101,12 +146,6 @@ 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
@@ -125,10 +164,10 @@ static_exe_robin_desktop: $(EXEFILE)
 all: desktop
 
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -o $@ $(DYN_LIBS)
+	$(CXX) $(LDFLAG) $^ -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)
+	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -Wl,-Bstatic $(DYN_LIBS_FOR_STATIC)
 
 obj/%.o: %.cpp $(HFILE)
 	$(CXX) $(CXXFLAG) -c $< -o $@ -Isrc -I$(HTSLIB_INC) -I$(BOOST_INC)