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1.11
date	2013.03.02.20.49.59;	author svnexp;	state Exp;
branches;
next	1.10;

1.10
date	2012.11.17.05.54.53;	author svnexp;	state Exp;
branches;
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1.9
date	2010.01.08.01.30.20;	author pgollucci;	state Exp;
branches;
next	1.8;

1.8
date	2006.12.26.12.46.33;	author linimon;	state Exp;
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1.7
date	2006.05.03.23.26.35;	author edwin;	state Exp;
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1.6
date	2006.01.09.03.25.02;	author edwin;	state Exp;
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1.5
date	2003.09.24.11.32.44;	author edwin;	state Exp;
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1.4
date	2003.02.21.11.01.38;	author knu;	state Exp;
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1.3
date	2002.11.05.01.44.12;	author edwin;	state Exp;
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1.2
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1.1
date	2002.09.10.13.58.40;	author dinoex;	state Exp;
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desc
@@


1.11
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/313250
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@# Created by: Tony Maher <tonym@@biolateral.com.au>
# $FreeBSD: head/biology/wise/Makefile 313250 2013-03-02 14:50:25Z miwi $

PORTNAME=	wise
PORTVERSION=	2.4.1
CATEGORIES=	biology
MASTER_SITES=	http://www.ebi.ac.uk/~birney/wise2/
DISTNAME=	${PORTNAME}${PORTVERSION}

MAINTAINER=	ports@@FreeBSD.org
COMMENT=	Intelligent algorithms for DNA searches

OPTIONS_DEFINE=	DOCS EXAMPLES

BUILD_WRKSRC=	${WRKSRC}/src

USE_GNOME=	glib20
MAKEFILE=	makefile
MAKE_JOBS_SAFE=	yes

SUB_FILES=	pkg-message

PORTDOCS=	*
PORTEXAMPLES=	*
PLIST_FILES=	${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,}
PLIST_DIRS=	%%DATADIR%%

#
# Actually want an 'ALL_TARGET = all perl' which then requires
# 'USE_PERL5= yes' but the perl sub-build is currently broken.
# The perl stuff is only so you can use the base libraries/functions
# from perl scripts.  This is extra, independent functionality for the
# port and not required for the base system which are C applications.
# When the perl part is fixed, it will require an install line
# something like '@@cd ${WRKSRC}/perl/Wise2; ${MAKE} install'
#

BINFILES=	dba dnal estwise estwisedb genewise genewisedb promoterwise \
		psw pswdb scanwise scanwise_server
DATAFILES=	BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \
		cb.tmf codon.table gene.stat gon120.bla gon160.bla \
		gon200.bla gon250.bla gon350.bla human.gf human.gp \
		human.stats idenity.bla methods pb.gf pombe.gf tm.pri \
		wise.2 wise.per worm.gf

.include <bsd.port.options.mk>

post-patch:
	@@${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \
		${REINPLACE_CMD} -e \
		's|^CC =|CC ?=| ; \
		 s|^CFLAGS =|CFLAGS +=| ; \
		 s|-O[0-9] | | ; \
		 s|-g | | ; \
		 s|-g[0-9] | | ; \
		 s|-lpthread|-pthread| ; \
		 s|glib-config|pkg-config glib-2.0| ; \
		 /welcome.csh/s|^|#|'

do-install:
.for i in ${BINFILES}
	(cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin)
.endfor
	@@${MKDIR} ${DATADIR}
.for i in ${DATAFILES}
	(cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR})
.endfor
.if ${PORT_OPTIONS:MDOCS}
	@@${MKDIR} ${DOCSDIR}
	@@(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR})
.endif
.if ${PORT_OPTIONS:MEXAMPLES}
	 @@${MKDIR} ${EXAMPLESDIR}
	@@(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
.endif
	@@${CAT} ${PKGMESSAGE}

.include <bsd.port.mk>
@


1.10
log
@Switch exporter over
@
text
@d1 2
a2 6
# New ports collection makefile for:	wise
# Date created:				26 February 2002
# Whom:					Tony Maher <tonym@@biolateral.com.au>
#
# $FreeBSD: head/biology/wise/Makefile 300895 2012-07-14 12:56:14Z beat $
#
d5 1
a5 1
PORTVERSION=	2.2.0
d7 1
a7 1
MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
d13 5
a17 2
WRKTOP=		${WRKDIR}/${DISTNAME}
WRKSRC=		${WRKTOP}/src
d19 2
d23 5
d38 21
a58 40
BINFILES=	dba dnal estwise estwisedb genewise genewisedb \
		genomewise psw pswdb
DATAFILES=	BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \
		aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \
		gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \
		gon350.bla human.gf human.gp human.stats idenity.bla \
		methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf
DOCFILES=	README apiend.tex appendix.tex dynamite.tex \
		genewise21.eps genewise6.eps gettex.pl makefile \
		wise2.tex wise2api.tex wise3arch.tex
EXFILES=	README db.hmm hn_est.fa human.genomic \
		keratin_intron.human keratin_intron.mouse pep.fa \
		road.pep rrm.HMM vav.dna xeno.cdna xeno.pep

#
# Top level makefile does not respect CFLAGS.  Fixing it means
# having to fix some of the sub-directory makefiles.
# Note: some makefiles are ok and know that '-c' does not belong
# in CFLAGS and are part of the rule.
#

post-configure:
	@@${REINPLACE_CMD} \
		-e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \
		-e s'#\tcsh welcome.csh##;' \
		${WRKSRC}/${MAKEFILE}
	@@${REINPLACE_CMD} \
		-e s'#CFLAGS) $?#CFLAGS) -c $?#;' \
		${WRKSRC}/base/${MAKEFILE}
	@@${REINPLACE_CMD} \
		-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
		${WRKSRC}/dynlibsrc/${MAKEFILE}
	@@${REINPLACE_CMD} \
		-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
		-e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \
		-e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \
		-e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \
		-e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \
		-e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \
		${WRKSRC}/models/${MAKEFILE}
d61 2
a62 2
.for file in ${BINFILES}
	@@${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin
d65 2
a66 2
.for file in ${DATAFILES}
	@@${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR}
d68 1
a68 1
.if !defined(NOPORTDOCS)
d70 3
a72 3
.for file in ${DOCFILES}
	@@${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR}
.endfor
d74 1
a74 4
.for file in ${EXFILES}
	@@${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR}
.endfor

a75 2

post-install:
@


1.9
log
@- SBU_FILES += pkg-message

PR:             ports/142409
Submitted by:   Sevan Janiyan <venture37@@geeklan.co.uk>
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.8
log
@Reset tonymaher@@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:		portmgr
@
text
@d20 1
d94 1
a94 1
	@@${SED} -E -e 's#PREFIX#${PREFIX}#' -e '/(^\[|]$$)/d' ${PKGMESSAGE}
@


1.7
log
@Remove USE_REINPLACE from all categories starting with B
@
text
@d14 1
a14 1
MAINTAINER=	tonymaher@@optusnet.com.au
@


1.6
log
@Fix maintainer address

    From: Tony Maher <anthony.maher@@uts.edu.au>
    To: Edwin Groothuis <edwin@@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:	Tony Maher <anthony.maher@@uts.edu.au>
@
text
@a18 1
USE_REINPLACE=	yes
@


1.5
log
@Port update (maintainer): biology/wise

	Fenner's porsurvey show wise no longer available at original
	site.  Original site readme shows it has moved so update
	the MASTER_SITES accordingly.

PR:		ports/57154
Submmited by:	Tony Maher <tonymaher@@optushome.com.au>
@
text
@d14 1
a14 1
MAINTAINER=	tonym@@biolateral.com.au
@


1.4
log
@De-pkg-comment.
@
text
@d11 1
a11 1
MASTER_SITES=	ftp://ftp.sanger.ac.uk/pub/birney/wise2/
@


1.3
log
@Modify replace RE to match syntax of sed now ("\)" -> ")"
Noticed by: bento
@
text
@d15 1
@


1.2
log
@PERL -> REINPLACE
And some ports have USE_PERL5=yes now.
@
text
@d58 1
a58 1
		-e s'#CFLAGS\) $?#CFLAGS\) -c $?#;' \
d61 1
a61 1
		-e s'#INCFLAGS\) $?#INCFLAGS\) -c $?#;' \
d64 6
a69 6
		-e s'#INCFLAGS\) $?#INCFLAGS\) -c $?#;' \
		-e s'#CFLAGS\) estwise.c#CFLAGS\) -c estwise.c#;' \
		-e s'#CFLAGS\) estwiseb.c#CFLAGS\) -c estwiseb.c#;' \
		-e s'#CFLAGS\) estwisedb.c#CFLAGS\) -c estwisedb.c#;' \
		-e s'#CFLAGS\) genewise.c#CFLAGS\) -c genewise.c#;' \
		-e s'#CFLAGS\) genewisedb.c#CFLAGS\) -c genewisedb.c#;' \
@


1.1
log
@"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."
@
text
@d18 1
d53 1
a53 1
	@@${PERL} -pi.orig \
d57 1
a57 1
	@@${PERL} -pi.orig \
d60 1
a60 1
	@@${PERL} -pi.orig \
d63 1
a63 1
	@@${PERL} -pi.orig \
@

