uchime: Replace mk script with a generic Makefile

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Aug 17 15:19:42 2018 -0500
Changeset:	7c9d0d425db7377e500fcacdcba1a142f19163e8

Modified Files:
	uchime/Makefile
Added Files:
	uchime/files/Makefile

Log Message:
uchime: Replace mk script with a generic Makefile

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7c9d0d425db7377e500fcacdcba1a142f19163e8

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 uchime/Makefile       |  3 ++-
 uchime/files/Makefile | 30 ++++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diffs:
diff --git a/uchime/Makefile b/uchime/Makefile
index b25b71f18d..fbf1511d05 100644
--- a/uchime/Makefile
+++ b/uchime/Makefile
@@ -22,7 +22,7 @@
 
 DISTNAME=	uchime4.2.40_src
 PKGNAME=	uchime-${PORTVERSION}
-CATEGORIES=	wip
+CATEGORIES=	biology
 MASTER_SITES=	http://drive5.com/uchime/
 
 MAINTAINER=	dsiercks%uwm.edu@localhost
@@ -33,6 +33,7 @@ LICENSE=	public-domain
 
 # Test and change if necessary.
 # MAKE_JOBS_SAFE=	no
+MAKE_FILE=	${FILESDIR}/Makefile
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
diff --git a/uchime/files/Makefile b/uchime/files/Makefile
new file mode 100755
index 0000000000..7bf7c1185e
--- /dev/null
+++ b/uchime/files/Makefile
@@ -0,0 +1,30 @@
+
+BIN =	uchime
+OBJS =	addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o
+
+CXXFLAGS ?=	-O3 -msse2 -mfpmath=sse
+CXXFLAGS +=	-D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+
+MKDIR ?=	mkdir
+INSTALL ?=	install
+PREFIX ?=	/usr/local
+DESTDIR ?=	.
+STRIP ?=	strip
+
+clean:
+	rm -f *.o mk.stdout mk.stderr tmp.stderr
+
+all: ${BIN}
+
+${BIN}: ${OBJS}
+	${CXX} -o ${BIN} ${OBJS} ${LDFLAGS}
+
+%.o: %.c:
+	${CXX} -c ${CXXFLAGS} $<
+
+install:
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c ${BIN} ${DESTDIR}${PREFIX}/bin
+
+install-strip: install
+	${STRIP} ${DESTDIR}${PREFIX}/bin/${BIN}