Merge pull request #4 from pb-cdunn/better-makefile

simpler GNUmakefile

GNUmakefile

@@ -1,61 +1,25 @@
-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result
-
-ALL = daligner daligner_p HPCdaligner HPCmapper LAsort LAmerge LAsplit LAcat LAshow LAcheck LA4Falcon DB2Falcon DB.so
-
-all: $(ALL)
-
-daligner: daligner.c filter.c filter.h align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o daligner daligner.c filter.c align.c DB.c QV.c -lpthread -lm
-
-daligner_p: daligner.c filter.c filter.h align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o daligner_p daligner.c filter.c align.c DB.c QV.c -lpthread -lm -DFALCON_DALIGNER_P
-
-HPCdaligner: HPCdaligner.c DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o HPCdaligner HPCdaligner.c DB.c QV.c -lm
-
-HPCmapper: HPCmapper.c DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o HPCmapper HPCmapper.c DB.c QV.c -lm
-
-LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm
-
-LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm
-
-LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm
-
-LA4Falcon: LA4Falcon.c align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LA4Falcon LA4Falcon.c align.c DB.c QV.c -lm
-
-LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm
-
-LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm
-
-LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm
-
-DB2Falcon: DB2Falcon.c DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o DB2Falcon DB2Falcon.c DB.c QV.c -lm
-
-DB.so: DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -shared -fPIC -o DB.so DB.c QV.c -lm
-
+THISDIR:=$(abspath $(dir $(lastword ${MAKEFILE_LIST})))
+CFLAGS+= -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result
+CPPFLAGS+= -MMD -MP -I${THISDIR}/../DAZZ_DB
+LDLIBS+= -ldazzdb -lm -lpthread
+LDFLAGS+= -L${THISDIR}/../DAZZ_DB
+MOST = daligner HPCdaligner HPCmapper LAsort LAmerge LAsplit LAcat LAshow LAcheck LA4Falcon DB2Falcon
+ALL:=${MOST} daligner_p
+vpath %.c ${THISDIR}
+vpath %.a ${THISDIR}/../DAZZ_DB
+
+all: ${ALL}
+daligner: filter.o
+daligner_p: filter_p.o
+${ALL}: align.o
 
 clean:
-	rm -f $(ALL)
-	rm -f LAupgrade.Dec.31.2014
-	rm -f daligner.tar.gz
-
-LAupgrade.Dec.31.2014: LAupgrade.Dec.31.2014.c align.c align.h DB.c DB.h QV.c QV.h
-	gcc $(CFLAGS) -o LAupgrade.Dec.31.2014 LAupgrade.Dec.31.2014.c align.c DB.c QV.c -lm
-
+	rm -f ${ALL}
+	rm -f ${DEPS}
+	rm -fr *.dSYM *.o
 
-install:
-	cp $(ALL) ~/bin
+.PHONY: clean all
 
-package:
-	make clean
-	tar -zcf daligner.tar.gz README *.h *.c Makefile
+SRCS:=$(notdir $(wildcard ${THISDIR}/*.c))
+DEPS:=$(patsubst %.c,%.d,${SRCS})
+-include ${DEPS}

README_PB.md

@@ -0,0 +1,8 @@
+We have removed DB and QV files, since there are identical in DAZZ_DB.
+
+Now, this package will not build unless the DAZZ_DB directory is supplied.
+
+    CPPFLAGS+= -Idazzdb-build-dir
+    LDFLAGS+= -Ldazzdb-build-dir
+
+For now, we use a relative path, `../DAZZ_DB`, assuming we are both submodules.

daligner_p.c

@@ -0,0 +1 @@
+#include "daligner.c"

filter_p.c

@@ -0,0 +1,2 @@
+#define FALCON_DALIGNER_P
+#include "filter.c"