Date: Sun, 15 Apr 2018 17:45:52 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r467402 - in head/biology: . smithwaterman smithwaterman/files Message-ID: <201804151745.w3FHjqBT012781@repo.freebsd.org>
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Author: jwb Date: Sun Apr 15 17:45:52 2018 New Revision: 467402 URL: https://svnweb.freebsd.org/changeset/ports/467402 Log: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15072 Added: head/biology/smithwaterman/ head/biology/smithwaterman/Makefile (contents, props changed) head/biology/smithwaterman/distinfo (contents, props changed) head/biology/smithwaterman/files/ head/biology/smithwaterman/files/Makefile (contents, props changed) head/biology/smithwaterman/pkg-descr (contents, props changed) head/biology/smithwaterman/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Apr 15 17:04:29 2018 (r467401) +++ head/biology/Makefile Sun Apr 15 17:45:52 2018 (r467402) @@ -111,6 +111,7 @@ SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust + SUBDIR += smithwaterman SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE Added: head/biology/smithwaterman/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/smithwaterman/Makefile Sun Apr 15 17:45:52 2018 (r467402) @@ -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> Added: head/biology/smithwaterman/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/smithwaterman/distinfo Sun Apr 15 17:45:52 2018 (r467402) @@ -0,0 +1,3 @@ +TIMESTAMP = 1523600109 +SHA256 (ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz) = 8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8 +SIZE (ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz) = 39190 Added: head/biology/smithwaterman/files/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/smithwaterman/files/Makefile Sun Apr 15 17:45:52 2018 (r467402) @@ -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) Added: head/biology/smithwaterman/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/smithwaterman/pkg-descr Sun Apr 15 17:45:52 2018 (r467402) @@ -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 Added: head/biology/smithwaterman/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/smithwaterman/pkg-plist Sun Apr 15 17:45:52 2018 (r467402) @@ -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
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