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(-)biology/fasta3/Makefile (-34 / +37 lines)
Lines 2-8 Link Here
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# $FreeBSD: head/biology/fasta3/Makefile 327709 2013-09-20 15:55:44Z bapt $
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# $FreeBSD: head/biology/fasta3/Makefile 327709 2013-09-20 15:55:44Z bapt $
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PORTNAME=	fasta3
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PORTNAME=	fasta3
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PORTVERSION=	36.3.6
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PORTVERSION=	36.3.6d
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CATEGORIES=	biology
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CATEGORIES=	biology
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MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
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MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
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DISTNAME=	fasta-${PORTVERSION}
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DISTNAME=	fasta-${PORTVERSION}
Lines 10-68 Link Here
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MAINTAINER=	ports@FreeBSD.org
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MAINTAINER=	ports@FreeBSD.org
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COMMENT=	Collection of programs for searching DNA and protein databases
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COMMENT=	Collection of programs for searching DNA and protein databases
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OPTIONS_DEFINE=	DOCS EXAMPLES
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NO_CDROM=	May not be sold or incorporated into a commercial product
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NO_CDROM=	May not be sold or incorporated into a commercial product
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WRKSRC=		${WRKDIR}/${DISTNAME}
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WRKSRC=		${WRKDIR}/${DISTNAME}
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BUILD_WRKSRC=	${WRKSRC}/src
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BUILD_WRKSRC=	${WRKSRC}/src
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INSTALL_WRKSRC=	${BUILD_WRKSRC}
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INSTALL_WRKSRC=	${BUILD_WRKSRC}
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SUB_FILES=	pkg-message
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MAKEFILE=	Makefile.freebsd
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MAKEFILE=	Makefile.freebsd
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MAKE_ENV=	THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \
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		FASTA_HOST="$$(${UNAME} -n)"
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XDIR=		${PREFIX}/bin
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SUB_FILES=	pkg-message
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FASTA_HOST!=	/usr/bin/uname -n
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MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
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PLIST_SUB=	VER="${PORTVERSION:R:R}"
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		FASTA_HOST='"${FASTA_HOST}"'
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FASTA3_DOCS=	README.versions \
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MAN1_LINKS=	fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \
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		ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \
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		tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1
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MAN1_FILES=	fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
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DOC_FILES=	README.versions \
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		fasta_func.doc readme.* fasta.defaults \
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		fasta_func.doc readme.* fasta.defaults \
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		fasta.options fasta_versions.html changes*.html
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		fasta.options fasta_versions.html changes*.html
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DATA=		data/*.mat
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DATA=		data/*.mat
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EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
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EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
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MAN1=		fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
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.include <bsd.port.options.mk>
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MLINKS=		fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
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		fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
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		fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
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		fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
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		fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
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PLIST_SUB=	VER=${PORTVERSION:R:R}
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NO_STAGE=	yes
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post-patch:
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post-patch:
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	@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
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	@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
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post-install:
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post-install:
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	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
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	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin)
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	${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
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	(cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \
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	@ ${MKDIR} ${DATADIR}
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		${STAGEDIR}${PREFIX}/etc/fastlibs.sample)
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	@${MKDIR} ${STAGEDIR}${DATADIR}
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.for data in ${DATA}
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.for data in ${DATA}
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	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
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	(cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR})
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.endfor
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.endfor
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	@ ${MKDIR} ${EXAMPLESDIR}
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.for manpage in ${MAN1_FILES}
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.for ex in ${EXAMPLES}
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	(cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \
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	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
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		${STAGEDIR}${MAN1PREFIX}/man/man1)
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.endfor
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.for links in ${MAN1_LINKS}
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	(${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links})
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.endfor
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.endfor
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.for manpage in ${MAN1}
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	@${MKDIR} ${STAGEDIR}${DOCSDIR}
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	${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
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.for i in COPYRIGHT FASTA_LIST README
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	(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR})
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.endfor
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.endfor
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.if !defined(NOPORTDOCS)
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.for docfile in ${DOC_FILES}
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	@ ${MKDIR} ${DOCSDIR}
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	(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR})
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	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
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.endfor
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	${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
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	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
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	${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
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.for ex in ${EXAMPLES}
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.for docfile in ${FASTA3_DOCS}
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	(cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR})
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	@ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
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.endfor
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.endfor
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.endif
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	@ ${CAT} ${PKGMESSAGE}
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.include <bsd.port.mk>
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.include <bsd.port.mk>
(-)biology/fasta3/distinfo (-2 / +2 lines)
Lines 1-2 Link Here
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SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
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SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
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SIZE (fasta-36.3.6.tar.gz) = 995298
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SIZE (fasta-36.3.6d.tar.gz) = 997714
(-)biology/fasta3/files/patch-Makefile.freebsd (-1 / +1 lines)
Lines 13-19 Link Here
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 BIN = ../bin
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 BIN = ../bin
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-XDIR =		/usr/local/bin
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-XDIR =		/usr/local/bin
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+XDIR =		${LOCALBASE}/bin
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+XDIR?=		${LOCALBASE}/bin
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 LIB_M+=		-lm
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 LIB_M+=		-lm
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(-)biology/fasta3/pkg-plist (-54 / +75 lines)
Lines 17-27 Link Here
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bin/tfastx%%VER%%
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bin/tfastx%%VER%%
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bin/tfasty%%VER%%
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bin/tfasty%%VER%%
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etc/fastlibs.sample
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etc/fastlibs.sample
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%%PORTDOCS%%%%DOCSDIR%%/README
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man/man1/fasta36.1.gz
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man/man1/fastf3.1.gz
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man/man1/fastf35.1.gz
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man/man1/fastm35.1.gz
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man/man1/fasts3.1.gz
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man/man1/fasts35.1.gz
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man/man1/fastx35.1.gz
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man/man1/fasty35.1.gz
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man/man1/ggsearch35.1.gz
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man/man1/lalign35.1.gz
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man/man1/map_db.1.gz
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man/man1/prfx35.1.gz
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man/man1/prss3.1.gz
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man/man1/prss35.1.gz
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man/man1/ps_lav.1.gz
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man/man1/ssearch35.1.gz
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man/man1/tfasta35.1.gz
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man/man1/tfastf35.1.gz
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man/man1/tfasts35.1.gz
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man/man1/tfastx35.1.gz
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man/man1/tfasty35.1.gz
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%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
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%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
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%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
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%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
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%%PORTDOCS%%%%DOCSDIR%%/README
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%%PORTDOCS%%%%DOCSDIR%%/README.versions
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%%PORTDOCS%%%%DOCSDIR%%/README.versions
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%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
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%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
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%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
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%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
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%%PORTDOCS%%%%DOCSDIR%%/fasta.options
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%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
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%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
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%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
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%%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
Lines 33-89 Link Here
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%%PORTDOCS%%%%DOCSDIR%%/readme.v35
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%%PORTDOCS%%%%DOCSDIR%%/readme.v35
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%%PORTDOCS%%%%DOCSDIR%%/readme.v36
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%%PORTDOCS%%%%DOCSDIR%%/readme.v36
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%%PORTDOCS%%%%DOCSDIR%%/readme.w32
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%%PORTDOCS%%%%DOCSDIR%%/readme.w32
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%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
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%%PORTDOCS%%%%DOCSDIR%%/fasta.options
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
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%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
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%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
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%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
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%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
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%%EXAMPLESDIR%%/dyr_human.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
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%%EXAMPLESDIR%%/egmsmg.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
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%%EXAMPLESDIR%%/gstt1_drome.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
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%%EXAMPLESDIR%%/gtm1_human.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
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%%EXAMPLESDIR%%/gtt1_drome.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
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%%EXAMPLESDIR%%/h10_human.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
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%%EXAMPLESDIR%%/hahu.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
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%%EXAMPLESDIR%%/lcbo.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
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%%EXAMPLESDIR%%/m1r.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
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%%EXAMPLESDIR%%/m2.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
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%%EXAMPLESDIR%%/mchu.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
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%%EXAMPLESDIR%%/mgstm1.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
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%%EXAMPLESDIR%%/ms1.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
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%%EXAMPLESDIR%%/musplfm.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
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%%EXAMPLESDIR%%/mwkw.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
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%%EXAMPLESDIR%%/mwrtc1.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
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%%EXAMPLESDIR%%/myosin_bp.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
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%%EXAMPLESDIR%%/n0.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
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%%EXAMPLESDIR%%/n1.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
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%%EXAMPLESDIR%%/n2.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
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%%EXAMPLESDIR%%/n2s.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
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%%EXAMPLESDIR%%/n2t.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
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%%EXAMPLESDIR%%/ngt.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
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%%EXAMPLESDIR%%/ngts.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
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%%EXAMPLESDIR%%/oohu.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
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%%EXAMPLESDIR%%/prio_atepa.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
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%%EXAMPLESDIR%%/qrhuld.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
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%%EXAMPLESDIR%%/titin_hum.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
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%%EXAMPLESDIR%%/xurt8c.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
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%%EXAMPLESDIR%%/xurtg.aa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
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%%EXAMPLESDIR%%/mgstm1.lc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
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%%EXAMPLESDIR%%/xurt8c.lc
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
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%%EXAMPLESDIR%%/bovgh.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
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%%EXAMPLESDIR%%/bovprl.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
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%%EXAMPLESDIR%%/gst.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
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%%EXAMPLESDIR%%/hsgstm1b.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
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%%EXAMPLESDIR%%/humgstd.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
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%%EXAMPLESDIR%%/mgstm1.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
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%%EXAMPLESDIR%%/mgstm1_genclone.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
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%%EXAMPLESDIR%%/mgtt2_x.seq
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%%EXAMPLESDIR%%/titin_hum.seq
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%%EXAMPLESDIR%%/mu.lib
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%%EXAMPLESDIR%%/n2_fs.lib
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%%EXAMPLESDIR%%/n_fs.lib
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%%EXAMPLESDIR%%/prot_test.lib
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%%DATADIR%%/blosum45.mat
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%%DATADIR%%/blosum45.mat
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%%DATADIR%%/blosum50.mat
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%%DATADIR%%/blosum50.mat
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%%DATADIR%%/blosum62.mat
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%%DATADIR%%/blosum62.mat
Lines 97-102 Link Here
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%%DATADIR%%/pam250.mat
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%%DATADIR%%/pam250.mat
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%%DATADIR%%/rna.mat
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%%DATADIR%%/rna.mat
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%%DATADIR%%/vtml160.mat
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%%DATADIR%%/vtml160.mat
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%%PORTDOCS%%@dirrm %%DOCSDIR%%
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@dirrm %%EXAMPLESDIR%%
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@dirrm %%DATADIR%%
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@dirrm %%DATADIR%%
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%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
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%%PORTDOCS%%@dirrm %%DOCSDIR%%

Return to bug 181883