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(-)Makefile (-19 / +11 lines)
Lines 2-11 Link Here
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# $FreeBSD$
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# $FreeBSD$
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PORTNAME=	phrap
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PORTNAME=	phrap
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PORTVERSION=	0.990329
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PORTVERSION=	1.090518
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CATEGORIES=	biology
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CATEGORIES=	biology
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MASTER_SITES=	# put the tarball manually
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MASTER_SITES=	# put the tarball manually
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DISTFILES=	distrib.tar.Z
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DISTFILES=	distrib.tar.gz
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DIST_SUBDIR=	${PORTNAME}
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DIST_SUBDIR=	${PORTNAME}
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MAINTAINER=	mzaki@m.u-tokyo.ac.jp
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MAINTAINER=	mzaki@m.u-tokyo.ac.jp
Lines 19-37 Link Here
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NO_WRKSUBDIR=	yes
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NO_WRKSUBDIR=	yes
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MAKEFILE=	makefile
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MAKEFILE=	makefile
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ALL_TARGET=	all manyreads
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ALL_TARGET=	all
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BINARIES=	cluster cross_match cross_match.manyreads loco \
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BINARIES=	calf_merge cluster cross_match loco phrap swat
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		phrap phrap.longreads phrap.manyreads swat
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SCRIPTS=	phrapview
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SCRIPTS=	phrapview
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.for f in ${BINARIES} ${SCRIPTS}
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PLIST_FILES+=	bin/${f}
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.endfor
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PORTDATA=	BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq
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PORTDATA=	BLOSUM50 BLOSUM62 PAM250 mat50 mat70 mb_matrix penalty2 vector.seq
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PORTDOCS=	general.doc phrap.doc swat.doc
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PORTDOCS=	general.doc phrap.doc swat.doc
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NO_STAGE=	yes
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.include <bsd.port.pre.mk>
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.include <bsd.port.pre.mk>
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.for f in ${DISTFILES}
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.for f in ${DISTFILES}
Lines 42-62 Link Here
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do-install:
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do-install:
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.for f in ${BINARIES}
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.for f in ${BINARIES}
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	@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
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	@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/
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	@${CHMOD} a-r ${PREFIX}/bin/${f} # as required by the agreement
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.endfor
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.endfor
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.for f in ${SCRIPTS}
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.for f in ${SCRIPTS}
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	@${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/
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	@${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/
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.endfor
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.endfor
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	@${MKDIR} ${DATADIR}
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	@${MKDIR} ${STAGEDIR}${DATADIR}
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.for f in ${PORTDATA}
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.for f in ${PORTDATA}
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	@${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}
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	@${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}
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.endfor
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.endfor
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.if ${PORT_OPTIONS:MDOCS}
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	@${MKDIR} ${STAGEDIR}${DOCSDIR}
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	@${MKDIR} ${DOCSDIR}
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.for f in ${PORTDOCS}
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.for f in ${PORTDOCS}
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	@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
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	@${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR}
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.endfor
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.endfor
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.endif
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.include <bsd.port.post.mk>
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.include <bsd.port.post.mk>
(-)distinfo (-2 / +3 lines)
Lines 1-2 Link Here
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SHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc
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MD5 (phrap/distrib.tar.gz) = 93ef3d1cca4d1a70ed16511d30a355ab
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SIZE (phrap/distrib.tar.Z) = 366163
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SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665
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SIZE (phrap/distrib.tar.gz) = 333159
(-)files/patch-makefile (-19 / +5 lines)
Lines 1-9 Link Here
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--- makefile.orig	1999-03-11 15:13:20.000000000 +0900
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--- makefile.orig	2009-06-03 00:45:34.000000000 +0900
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+++ makefile	2007-12-11 13:19:39.000000000 +0900
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+++ makefile	2010-02-12 18:05:23.000000000 +0900
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@@ -23,8 +23,8 @@
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@@ -25,8 +25,8 @@
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 #*****************************************************************************/
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 # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
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 # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
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 #CC= icc
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 #CFLAGS= -O2 -wd266,880
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-CC= cc
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-CC= cc
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-CFLAGS= -O2
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-CFLAGS= -O2
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+CC?= cc
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+CC?= cc
Lines 11-27 Link Here
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 LFLAGS= -lm
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 LFLAGS= -lm
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 SWATOBJS= swat.o weibull.o
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 SWATOBJS= swat.o weibull.o
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@@ -55,11 +55,11 @@
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 manyreads:  
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 	touch swat.h;
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-	make CFLAGS="-O2 -DMANYREADS" phrap cross_match;
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+	make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match;
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 	mv phrap phrap.manyreads;
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 	mv cross_match cross_match.manyreads;
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 	touch swat.h;
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-	make CFLAGS="-O2 -DLONGREADS" phrap;
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+	make CFLAGS="$(CFLAGS) -DLONGREADS" phrap;
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 	mv phrap phrap.longreads;
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 	touch swat.h;
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 	make phrap cross_match;
(-)pkg-plist (+9 lines)
Line 0 Link Here
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@mode 111
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bin/calf_merge
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bin/cluster
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bin/cross_match
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bin/loco
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bin/phrap
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bin/phrapview
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bin/swat
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@mode

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