head	1.23;
access;
symbols
	RELEASE_5_EOL:1.22
	RELEASE_7_0_0:1.21
	RELEASE_6_3_0:1.21
	PRE_XORG_7:1.20
	RELEASE_4_EOL:1.20
	RELEASE_6_2_0:1.19
	RELEASE_6_1_0:1.19
	RELEASE_5_5_0:1.19
	RELEASE_6_0_0:1.19
	RELEASE_5_4_0:1.17
	RELEASE_4_11_0:1.17
	RELEASE_5_3_0:1.16
	RELEASE_4_10_0:1.13
	RELEASE_5_2_1:1.13
	RELEASE_5_2_0:1.13
	RELEASE_4_9_0:1.10
	RELEASE_5_1_0:1.9
	RELEASE_4_8_0:1.9
	RELEASE_5_0_0:1.8
	RELEASE_4_7_0:1.6
	RELEASE_4_6_2:1.5
	RELEASE_4_6_1:1.5
	RELEASE_4_6_0:1.5
	RELEASE_5_0_DP1:1.5
	RELEASE_4_5_0:1.4
	RELEASE_4_4_0:1.4
	RELEASE_4_3_0:1.1
	RELEASE_4_2_0:1.1;
locks; strict;
comment	@# @;


1.23
date	2008.07.24.12.17.11;	author pav;	state dead;
branches;
next	1.22;

1.22
date	2008.04.06.08.39.20;	author rafan;	state Exp;
branches;
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1.21
date	2007.10.28.21.42.23;	author miwi;	state Exp;
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1.20
date	2006.12.23.21.45.16;	author miwi;	state Exp;
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1.19
date	2005.04.29.22.14.29;	author jylefort;	state Exp;
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1.18
date	2005.04.28.19.01.41;	author jylefort;	state Exp;
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1.17
date	2004.10.28.21.01.05;	author kris;	state Exp;
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1.16
date	2004.09.19.01.28.23;	author kris;	state Exp;
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1.15
date	2004.07.02.09.53.25;	author vs;	state Exp;
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1.14
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1.13
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1.12
date	2003.10.14.12.18.50;	author daichi;	state Exp;
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1.11
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1.10
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1.9
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1.8
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1.7
date	2002.10.29.22.27.16;	author pat;	state Exp;
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1.6
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1.5
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1.4
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1.3
date	2001.06.01.06.04.45;	author obrien;	state Exp;
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1.2
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1.1
date	2000.10.10.02.57.20;	author jeh;	state Exp;
branches;
next	;


desc
@@


1.23
log
@- Delete biology/nab port after being marked DEPRECATED for three months

PR:		ports/125891
Submitted by:	M. L. Dodson <mldodson@@comcast.net> (maintainer)
@
text
@# New ports collection Makefile for: nab
# Date created:         Sept. 10, 2000
# Whom:                 M. L. Dodson <mldodson@@comcast.net>
#
# $FreeBSD: ports/biology/nab/Makefile,v 1.22 2008/04/06 08:39:20 rafan Exp $
#

PORTNAME=	nab
PORTVERSION=	5.1.2
PORTREVISION=	1
CATEGORIES=	biology
MASTER_SITES=	http://www.activesitedynamics.com/mldodson/

MAINTAINER=	mldodson@@comcast.net
COMMENT=	A language for macromolecules

BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
RUN_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp

DEPRECATED=	superseded by AmberTools (by same development group)

MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \
		CFLAGS="${CFLAGS}" OCFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"

MAN1=		nab.1
SUB_FILES=	pkg-message

BINARIES=	matmerge nab2c teLeap tss_main \
		matextract matmul transform tss_next \
		matgen nab tss_init

LIBRARIES=	cifparse.a libnab.a libsym.a

INCS=		defreal.h nab.h nabcode.h nabtypes.h

do-configure:
	@@${CP} ${FILESDIR}/config.h ${WRKSRC}

post-patch:
	@@${RM} -f ${WRKSRC}/examples/circle.c
	@@${RM} -f ${WRKSRC}/reslib/conf.lib.orig
	@@${RM} -f ${WRKSRC}/examples/program_7.nab.orig

do-build:
	@@cd ${WRKSRC} && \
		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} install
	@@cd ${WRKSRC}/test && \
		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test
	@@cd ${WRKSRC}/nss  && \
		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test

build-general-version:
	@@cd ${WRKSRC}/src && \
		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} beforerealinstall

do-install: build-general-version
	${MKDIR} ${DATADIR}/bin ${DATADIR}/include ${DATADIR}/lib
	cd ${WRKSRC}/test && ${RM} -f d01.pdb gbrna.pdb.lpdb rembed.out
	cd ${WRKSRC}/examples && ${RM} -f gcg10.pdb.save
	cd ${WRKSRC}/leap/parm && ${RM} -f leap.log
.if !defined(NOPORTDOCS)
	cd ${WRKSRC} && (${TAR} cf - benchmarks examples test | \
		(cd ${DATADIR}; ${TAR} xf -))
	${MKDIR} ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR}
.endif
	cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data leap | \
		(cd ${DATADIR}; ${TAR} xf -))
	${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${DATADIR}/*
	cd ${DATADIR} && ${LN} -sf ../NDB coords
	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin
.for f in ${INCS}
	${INSTALL_DATA} ${WRKSRC}/include/${f} ${PREFIX}/include
	cd ${DATADIR}/include && ${LN} -sf ${PREFIX}/include/${f} .
.endfor
	${INSTALL_DATA} ${WRKSRC}/config.h ${DATADIR}
	${INSTALL_MAN} ${WRKSRC}/doc/nab.1 ${MAN1PREFIX}/man/man1
.for f in ${BINARIES}
	cd ${DATADIR}/bin && ${LN} -sf ${PREFIX}/bin/${f} .
.endfor
.for f in ${LIBRARIES}
	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib
	cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} .
.endfor
.for f in blas.a lapack.a f2c.a
	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib
	${LN} ${DATADIR}/lib/${f} ${DATADIR}/lib/lib${f}
.endfor
	@@${CAT} ${PKGMESSAGE}

.include <bsd.port.mk>
@


1.22
log
@- Update maintainer's email
- Mark as deprecated

PR:		ports/122474
Submitted by:	M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.21
log
@- Allow build with AMD64
- Fix pkg-plist
- Bump PORTREVISION

PR:		117435
Submitted by:	"M. L. Dodson" <mldodson@@comcast.net> (maintainer)
@
text
@d3 1
a3 1
# Whom:                 M. L. Dodson <mldodson@@houston.rr.com>
d12 1
a12 1
MASTER_SITES=	http://www.scripps.edu/mb/case/
d14 1
a14 1
MAINTAINER=	mldodson@@houston.rr.com
d20 2
@


1.20
log
@- Update to 5.1.2
- Update maintainer mail adresse

PR:		ports/107118
Submitted by:	M. L. Dodson <bdodson@@houston.rr.com> (maintainer)
@
text
@d10 1
a19 2
ONLY_FOR_ARCHS=	i386

d85 1
@


1.19
log
@- Fix the packing list [1]
- Add a run dependency on ucpp
- Correct the NABHOME used in pre-install

PR:		ports/80457
Submitted by:	maintainer
Reported by:	pointyhat [1]
@
text
@d3 1
a3 1
# Whom:                 M. L. Dodson <bdodson@@scms.utmb.edu>
d9 1
a9 2
PORTVERSION=	5.0
PORTREVISION=	1
d11 1
a11 2
MASTER_SITES=	http://www.scripps.edu/case/ \
		http://siegfried.utmb.edu/bdodson/
d13 1
a13 1
MAINTAINER=	bdodson@@scms.utmb.edu
d22 1
a22 1
		CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
d27 3
a29 3
BINARIES=	matextract	matmul		teLeap		tss_main \
		matgen		nab		transform	tss_next \
		matmerge	nab2c		tss_init
d31 1
a31 1
LIBRARIES=	cifparse.a	libnab.a        libsym.a
d33 1
a33 1
INCS=	defreal.h	nab.h		nabcode.h	nabtypes.h
d35 1
a35 1
post-extract:
d41 1
d43 9
a51 1
pre-install:
d55 1
a55 1
do-install:
d58 2
d61 1
a61 1
	cd ${WRKSRC} && (${TAR} cf - benchmarks examples test peptide suppose | \
d84 1
a84 1
.for f in blas.a lapack.a
a86 2

post-install:
@


1.18
log
@- Update to 5.0
- Cleanups

PR:		ports/80372
Submitted by:	maintainer
@
text
@d10 1
d19 1
d50 1
a50 1
	cd ${WRKSRC}/test && ${RM} -f gbrna.pdb.lpdb rembed.out
@


1.17
log
@Now installs on FreeBSD 5.x.
@
text
@d9 1
a9 1
PORTVERSION=	4.6
d11 1
a11 2
MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
		http://www.scripps.edu/case/ \
d15 1
a15 2
COMMENT=	\
 "This is nab (nucleic acid builder), a language for macromolecules"
d21 2
a22 1
MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH}
d25 1
a25 2
MANCOMPRESSED=	yes
USE_REINPLACE=	yes
d27 3
a29 3
BINARIES=	matextract      matmul          teLeap          tss_main \
		matgen          nab             transform       tss_next \
		matmerge        nab2c           tss_init
d31 1
a31 1
LIBRARIES=	cifparse.a      libnab.a        libsym.a
d33 1
a33 1
INCS=	defreal.h       nab.h           nabcode.h       nabtypes.h
a37 4
pre-patch:
	@@${REINPLACE_CMD} -e 's,<malloc.h>,<stdlib.h>,' \
		${WRKSRC}/cifparse/cifparse.c

d39 1
a39 9
	@@${RM} -f ${WRKSRC}/examples/program_7.nab.orig
	@@${RM} -f ${WRKSRC}/examples/program_1.c \
		${WRKSRC}/examples/program_1.exe
	@@${RM} -f ${WRKSRC}/test/1ubq/a.exe
	@@${RM} -f ${WRKSRC}/test/1ubq/rattle_min.c
	@@${RM} -f ${WRKSRC}/test/1ubq/runleap.c
	@@${RM} -f ${WRKSRC}/test/*.exe
	@@${RM} -f ${WRKSRC}/tleap/utilMakeHelp.exe
	@@${RM} -f ${WRKSRC}/fd_data/abdna.dat.old
a40 4
	@@${RM} -f ${WRKSRC}/reslib/leap/parm94.dat~
	@@(cd ${WRKSRC}/reslib/leap && \
		${FIND} . -type f -print | ${GREP} -v '\./[a-zA-Z0-9]' | \
			${XARGS} ${RM} -f)
d44 1
a44 1
		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
d47 2
a48 4
	@@-${MKDIR} ${PREFIX}/share/nab
	@@-${MKDIR} ${PREFIX}/share/nab/bin
	@@-${MKDIR} ${PREFIX}/share/nab/include
	@@-${MKDIR} ${PREFIX}/share/nab/lib
d50 4
a53 4
	@@cd ${WRKSRC} && (${TAR} cf - examples test peptide suppose | \
		(cd ${PREFIX}/share/nab; ${TAR} xf -))
	@@-${MKDIR} ${PREFIX}/share/doc/nab
	${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab
d55 5
a59 6
	@@cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data | \
		(cd ${PREFIX}/share/nab; ${TAR} xf -))
	@@(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} nab; \
		${CHMOD} -R ugo+rX-w nab)
	@@-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords)
	${INSTALL_PROGRAM} ${WRKSRC}/bin/*     ${PREFIX}/bin
d61 2
a62 2
	${INSTALL_DATA}    ${WRKSRC}/include/${f} ${PREFIX}/include
	@@-(cd ${PREFIX}/share/nab/include && ${LN} -sf ${PREFIX}/include/${f} .)
d64 2
a65 4
	${INSTALL_DATA} ${WRKSRC}/config.h ${PREFIX}/share/nab/include
	${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib
	@@-cd ${WRKSRC}/doc && ${GZIP_CMD} ${MAN1}
	${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1
d67 1
a67 1
	@@cd ${PREFIX}/share/nab/bin && ${LN} -sf ../../../bin/${f} .
d70 5
a74 1
	@@cd ${PREFIX}/share/nab/lib && ${LN} -sf ../../../lib/${f} .
@


1.16
log
@BROKEN on 5.x: Does not compile

Approved by:    portmgr (self)
@
text
@a36 6
.include <bsd.port.pre.mk>

.if ${OSVERSION} >= 502126
BROKEN=		"Does not install on FreeBSD >= 5.x"
.endif

d99 1
a99 1
.include <bsd.port.post.mk>
@


1.15
log
@Update to 4.6

PR:		ports/68561
Submitted by:	maintainer
@
text
@d37 6
d105 1
a105 1
.include <bsd.port.mk>
@


1.14
log
@- update to 4.5.3
- remove version from pkg-descr

PR:		65972
Submitted by:	maintainer
@
text
@d9 1
a9 1
PORTVERSION=	4.5.3
a62 1
	@@${CP} ${WRKSRC}/config.h ${WRKSRC}/include/
d81 6
a86 2
	${INSTALL_DATA}    ${WRKSRC}/include/* ${PREFIX}/share/nab/include
	${INSTALL_DATA} ${WRKSRC}/lib/*     ${PREFIX}/lib
@


1.13
log
@${MASTER_SITES} are slow.  This patch adds a mirror site to help
fetch work more frequently.  This patch patches the Makefile from
PORTSDIR}/biology

PR:		58130
Submitted by:	MAINTAINER
@
text
@d9 1
a9 1
PORTVERSION=	4.5.2
d21 1
a21 1
ONLY_FOR_ARCHS= i386
d54 1
d63 1
d82 1
a82 1
	${INSTALL_DATA}    ${WRKSRC}/include/* ${PREFIX}/include
a90 3
.endfor
.for f in ${INCS}
	@@cd ${PREFIX}/share/nab/include && ${LN} -sf ../../../include/${f} .
@


1.12
log
@update biology/nab: 4.5.1 -> 4.5.2

PR:		57970
Submitted by:	M. L. Dodson <bdodson@@scms.utmb.edu> (maintainer)
@
text
@d12 2
a13 1
		http://www.scripps.edu/case/
@


1.11
log
@BROKEN: Does not fetch
@
text
@d9 1
a9 1
PORTVERSION=	4.5.1
a17 2
BROKEN=		Does not fetch

d44 13
a56 1
	@@rm -f ${WRKSRC}/examples/program_7.nab.orig
@


1.10
log
@update biology/nab: 4.4 -> 4.5.1

PR:		52786
Submitted by:	M. L. Dodson <bdodson@@scms.utmb.EDU> (maintainer)
@
text
@d18 2
@


1.9
log
@De-pkg-comment.
@
text
@d9 1
a9 1
PORTVERSION=	4.4
d15 6
a20 1
COMMENT=	This is nab (nucleic acid builder), a language for macromolecules
a23 1
USE_BISON=	yes
d30 1
a30 1
		matmerge        nab2c           tss_init        ucpp
d51 4
a54 4
	@@-mkdir -p ${PREFIX}/share/nab
	@@-mkdir -p ${PREFIX}/share/nab/bin
	@@-mkdir -p ${PREFIX}/share/nab/include
	@@-mkdir -p ${PREFIX}/share/nab/lib
d56 3
a58 3
	@@cd ${WRKSRC} && (tar cf - examples test peptide suppose | \
		(cd ${PREFIX}/share/nab; tar xf -))
	@@-mkdir -p ${PREFIX}/share/doc/nab
d61 2
a62 2
	@@cd ${WRKSRC} && (tar cf - dgdb reslib fd_data | \
		(cd ${PREFIX}/share/nab; tar xf -))
@


1.8
log
@PERL -> REINPLACE
Noticed on: bento
@
text
@d15 1
@


1.7
log
@Add another entry for MASTER_SITES and unbreak with latest version of bison

PR:		ports/44711
Submitted by:	maintainer
@
text
@d21 1
d35 1
a35 1
	@@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \
@


1.6
log
@upgrade to 4.4

PR:		40612
Submitted by:	maintainer
@
text
@d4 1
d6 1
d11 2
a12 1
MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/
@


1.5
log
@Remove #include <malloc.h>
@
text
@d7 1
a7 1
PORTVERSION=	4.3.2
d33 3
@


1.4
log
@This port require bison to build so add USE_BISON.
@
text
@d4 1
a4 1
# $FreeBSD: ports/biology/nab/Makefile,v 1.3 2001/06/01 06:04:45 obrien Exp $
d29 4
@


1.3
log
@Use proper POSIX syntax for `chown'.
@
text
@d4 1
a4 1
# $FreeBSD: ports/biology/nab/Makefile,v 1.2 2001/05/27 13:49:52 ijliao Exp $
d15 1
@


1.2
log
@upgrade to 4.3.2

PR:		27273
Submitted by:	maintainer
@
text
@d4 1
a4 1
# $FreeBSD: ports/biology/nab/Makefile,v 1.1 2000/10/10 02:57:20 jeh Exp $
d46 1
a46 1
	@@(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}.${SHAREGRP} nab; \
@


1.1
log
@Initiail version of nab (4.2)

PR:		21585
Submitted by:	M. L. Dodson <bdodson@@scms.utmb.EDU>
@
text
@d4 1
a4 1
# $FreeBSD$
d7 1
a7 1
PORTVERSION=	4.2
d13 2
a14 4
NO_WRKSUBDIR=	yes
MAKE_ENV+=	WRKSRC=${WRKSRC} PREFIX=${PREFIX} \
		NABHOME=${PREFIX}/share/nab ARCH= \
		INSTALL_MAN="${INSTALL_MAN}"
d18 8
a26 2
	@@${CP} ${FILESDIR}/Makefile ${WRKSRC}
	@@${CP} ${FILESDIR}/Makefile.doc ${WRKSRC}/doc/Makefile
d30 4
d35 5
a39 2
.if !defined(${NOPORTDOCS})
	@@cd ${WRKSRC} && (tar cf - examples test | \
d44 1
a44 1
	@@cd ${WRKSRC} && (tar cf - dgdb reslib | \
d48 15
a62 1
	@@-(cd ${PREFIX}/share/nab; ${RM} -f coords && ${LN} -s ../NDB coords)
a64 6
	@@(cd ${PREFIX}/bin; \
	${RM} -f nab && ${MV} ${PREFIX}/share/nab/bin/nab . ; \
	${RM} -f nab2c && ${MV} ${PREFIX}/share/nab/bin/nab2c . ; \
	${CHOWN} ${BINOWN}:${BINGRP} nab nab2c teLeap ; \
	strip nab nab2c teLeap ; \
	${RMDIR} ${PREFIX}/share/nab/bin)
a65 3

test:	all
	@@cd ${WRKSRC}/src && make test
@

