biology/smithwaterman: Smith-waterman-gotoh alignment algorithm

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15072

biology/Makefile

@@ -111,6 +111,7 @@
     SUBDIR += seqtools
     SUBDIR += sim4
     SUBDIR += slclust
+    SUBDIR += smithwaterman
     SUBDIR += ssaha
     SUBDIR += stacks
     SUBDIR += tRNAscan-SE

biology/smithwaterman/Makefile

@@ -0,0 +1,25 @@
+# $FreeBSD$
+
+PORTNAME=	smithwaterman
+DISTVERSION=	g20160702
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Smith-waterman-gotoh alignment algorithm
+
+LICENSE=	GPLv2
+
+USES=		gmake
+USE_LDCONFIG=	yes
+USE_GITHUB=	yes
+GH_ACCOUNT=	ekg
+GH_TAGNAME=	2610e259611ae4cde8f03c72499d28f03f6d38a7
+
+MAKEFILE=	${FILESDIR}/Makefile
+INSTALL_TARGET=	install-strip
+
+post-install:
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libsw.so.1 \
+		${STAGEDIR}${PREFIX}/lib/libsw.so
+
+.include <bsd.port.mk>

biology/smithwaterman/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1523600109
+SHA256 (ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz) = 8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8
+SIZE (ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz) = 39190

biology/smithwaterman/files/Makefile

@@ -0,0 +1,100 @@
+# =========================================
+# MOSAIK Banded Smith-Waterman Makefile
+# (c) 2009 Michael Stromberg & Wan-Ping Lee
+# =========================================
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+
+SOURCES= smithwaterman.cpp BandedSmithWaterman.cpp SmithWatermanGotoh.cpp Repeats.cpp LeftAlign.cpp IndelAllele.cpp
+OBJECTS= $(SOURCES:.cpp=.o) disorder.o
+OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
+
+# ----------------
+# compiler options
+# ----------------
+
+# Use ?= to allow overriding from the env or command-line, e.g.
+#
+#       make CXXFLAGS="-O3 -fPIC" install
+#
+# Package managers will override many of these variables automatically, so
+# this is aimed at making it easy to create packages (Debian packages,
+# FreeBSD ports, MacPorts, pkgsrc, etc.)
+
+CXX ?=		c++
+CXXFLAGS ?=	-O3
+CXXFLAGS +=	-fPIC
+DESTDIR ?=	stage
+PREFIX ?=	/usr/local
+STRIP ?=	strip
+INSTALL ?=	install -c
+MKDIR ?=	mkdir -p
+AR ?=		ar
+LN ?=		ln
+
+LDFLAGS:=	-Wl,-s
+BIN =		smithwaterman
+LIB =		libsw.a
+SOVERSION =	1
+SLIB =		libsw.so.$(SOVERSION)
+
+all: $(BIN) $(LIB) $(SLIB) sw.o
+
+.PHONY: all
+
+$(LIB): $(OBJECTS_NO_MAIN)
+	$(AR) rs $@ $(OBJECTS_NO_MAIN)
+
+$(SLIB): $(OBJECTS_NO_MAIN)
+	$(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJECTS_NO_MAIN)
+
+sw.o:  $(OBJECTS_NO_MAIN)
+	ld -r $^ -o sw.o -L.
+	@#$(CXX) $(CFLAGS) -c -o smithwaterman.cpp $(OBJECTS_NO_MAIN) -I.
+
+### @$(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $^ -I.
+$(BIN): $(OBJECTS)
+	$(CXX) $(CFLAGS) $^ -I. -o $@
+
+#smithwaterman: $(OBJECTS)
+#	$(CXX) $(CXXFLAGS) -o $@ $< -I.
+
+smithwaterman.o: smithwaterman.cpp disorder.o
+	$(CXX) $(CXXFLAGS) -c -o $@ smithwaterman.cpp -I.
+
+disorder.o: disorder.cpp disorder.h
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+BandedSmithWaterman.o: BandedSmithWaterman.cpp BandedSmithWaterman.h
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+SmithWatermanGotoh.o: SmithWatermanGotoh.cpp SmithWatermanGotoh.h disorder.o
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+Repeats.o: Repeats.cpp
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+LeftAlign.o: LeftAlign.cpp
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+IndelAllele.o: IndelAllele.cpp
+	$(CXX) $(CXXFLAGS) -c -o $@ $< -I.
+
+install: all
+	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
+	$(MKDIR) $(DESTDIR)$(PREFIX)/include/smithwaterman
+	$(MKDIR) $(DESTDIR)$(PREFIX)/lib
+	$(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin
+	$(INSTALL) *.h $(DESTDIR)$(PREFIX)/include/smithwaterman
+	$(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib
+
+install-strip: install
+	$(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) $(DESTDIR)$(PREFIX)/lib/$(SLIB)
+
+.PHONY: clean
+
+clean:
+	@echo "Cleaning up."
+	@rm -rf $(BIN) $(LIB) $(SLIB) $(OBJECTS) $(DESTDIR)

biology/smithwaterman/pkg-descr

@@ -0,0 +1,8 @@
+The Smith-Waterman algorithm performs local sequence alignment; that is, for
+determining similar regions between two strings of nucleic acid sequences or
+protein sequences. Instead of looking at the entire sequence, the
+Smith-Waterman algorithm compares segments of all possible lengths and
+optimizes the similarity measure.  Gotoh and Atschul added optimizations making
+it practical for larger problems.
+
+WWW: https://github.com/ekg/smithwaterman

biology/smithwaterman/pkg-plist

@@ -0,0 +1,12 @@
+bin/smithwaterman
+include/smithwaterman/BandedSmithWaterman.h
+include/smithwaterman/IndelAllele.h
+include/smithwaterman/LeftAlign.h
+include/smithwaterman/Mosaik.h
+include/smithwaterman/Repeats.h
+include/smithwaterman/SmithWatermanGotoh.h
+include/smithwaterman/convert.h
+include/smithwaterman/disorder.h
+lib/libsw.a
+lib/libsw.so
+lib/libsw.so.1