head	1.66;
access;
symbols
	RELEASE_8_3_0:1.62
	RELEASE_9_0_0:1.62
	RELEASE_7_4_0:1.61
	RELEASE_8_2_0:1.61
	RELEASE_6_EOL:1.60
	RELEASE_8_1_0:1.60
	RELEASE_7_3_0:1.58
	RELEASE_8_0_0:1.57
	RELEASE_7_2_0:1.54
	RELEASE_7_1_0:1.52
	RELEASE_6_4_0:1.52
	RELEASE_5_EOL:1.52
	RELEASE_7_0_0:1.48
	RELEASE_6_3_0:1.48
	PRE_XORG_7:1.47
	RELEASE_4_EOL:1.47
	RELEASE_6_2_0:1.47
	RELEASE_6_1_0:1.46
	RELEASE_5_5_0:1.46
	RELEASE_6_0_0:1.43
	RELEASE_5_4_0:1.42
	RELEASE_4_11_0:1.41
	RELEASE_5_3_0:1.39
	RELEASE_4_10_0:1.38
	RELEASE_5_2_1:1.37
	RELEASE_5_2_0:1.37
	RELEASE_4_9_0:1.35
	RELEASE_5_1_0:1.31
	RELEASE_4_8_0:1.31
	RELEASE_5_0_0:1.30
	RELEASE_4_7_0:1.30
	RELEASE_4_6_2:1.27
	RELEASE_4_6_1:1.27
	RELEASE_4_6_0:1.27
	RELEASE_5_0_DP1:1.26
	RELEASE_4_5_0:1.25
	RELEASE_4_4_0:1.24
	RELEASE_4_3_0:1.19
	RELEASE_4_2_0:1.10
	RELEASE_4_1_1:1.5;
locks; strict;
comment	@# @;


1.66
date	2012.11.17.05.54.51;	author svnexp;	state Exp;
branches;
next	1.65;

1.65
date	2012.10.01.14.55.55;	author wen;	state Exp;
branches;
next	1.64;

1.64
date	2012.10.01.14.45.16;	author tabthorpe;	state Exp;
branches;
next	1.63;

1.63
date	2012.06.01.05.16.28;	author dinoex;	state Exp;
branches;
next	1.62;

1.62
date	2011.05.02.12.44.26;	author makc;	state Exp;
branches;
next	1.61;

1.61
date	2010.12.04.07.30.34;	author ade;	state Exp;
branches;
next	1.60;

1.60
date	2010.04.07.01.16.50;	author wen;	state Exp;
branches;
next	1.59;

1.59
date	2010.03.28.06.31.36;	author dinoex;	state Exp;
branches;
next	1.58;

1.58
date	2010.02.05.11.34.36;	author dinoex;	state Exp;
branches;
next	1.57;

1.57
date	2009.08.14.08.33.22;	author miwi;	state Exp;
branches;
next	1.56;

1.56
date	2009.08.02.19.32.30;	author mezz;	state Exp;
branches;
next	1.55;

1.55
date	2009.07.31.13.49.17;	author dinoex;	state Exp;
branches;
next	1.54;

1.54
date	2009.03.14.15.16.07;	author miwi;	state Exp;
branches;
next	1.53;

1.53
date	2009.03.14.15.14.45;	author miwi;	state Exp;
branches;
next	1.52;

1.52
date	2008.04.17.17.06.48;	author pav;	state Exp;
branches;
next	1.51;

1.51
date	2008.04.17.01.31.22;	author rafan;	state Exp;
branches;
next	1.50;

1.50
date	2008.04.13.07.22.20;	author rafan;	state Exp;
branches;
next	1.49;

1.49
date	2008.03.23.16.44.04;	author miwi;	state Exp;
branches;
next	1.48;

1.48
date	2007.05.19.20.00.23;	author flz;	state Exp;
branches;
next	1.47;

1.47
date	2006.03.31.09.43.20;	author thierry;	state Exp;
branches;
next	1.46;

1.46
date	2006.02.23.10.34.51;	author ade;	state Exp;
branches;
next	1.45;

1.45
date	2006.02.02.23.12.04;	author marcus;	state Exp;
branches;
next	1.44;

1.44
date	2005.11.15.06.48.10;	author ade;	state Exp;
branches;
next	1.43;

1.43
date	2005.05.29.18.26.05;	author pav;	state Exp;
branches;
next	1.42;

1.42
date	2005.02.11.21.11.51;	author sem;	state Exp;
branches;
next	1.41;

1.41
date	2004.11.26.01.11.42;	author sem;	state Exp;
branches;
next	1.40;

1.40
date	2004.11.20.07.40.43;	author linimon;	state Exp;
branches;
next	1.39;

1.39
date	2004.06.23.08.20.21;	author vs;	state Exp;
branches;
next	1.38;

1.38
date	2004.02.04.05.18.49;	author marcus;	state Exp;
branches;
next	1.37;

1.37
date	2003.11.20.15.05.56;	author trevor;	state Exp;
branches;
next	1.36;

1.36
date	2003.11.20.13.51.33;	author trevor;	state Exp;
branches;
next	1.35;

1.35
date	2003.08.18.16.15.05;	author nork;	state Exp;
branches;
next	1.34;

1.34
date	2003.08.08.04.40.38;	author kris;	state Exp;
branches;
next	1.33;

1.33
date	2003.08.07.09.29.17;	author kris;	state Exp;
branches;
next	1.32;

1.32
date	2003.07.11.18.16.11;	author nork;	state Exp;
branches;
next	1.31;

1.31
date	2003.03.07.05.56.41;	author ade;	state Exp;
branches;
next	1.30;

1.30
date	2002.09.27.08.58.19;	author wjv;	state Exp;
branches;
next	1.29;

1.29
date	2002.09.20.20.45.20;	author kris;	state Exp;
branches;
next	1.28;

1.28
date	2002.07.05.10.09.31;	author wjv;	state Exp;
branches;
next	1.27;

1.27
date	2002.05.17.09.24.32;	author kris;	state Exp;
branches;
next	1.26;

1.26
date	2002.03.25.09.19.17;	author sobomax;	state Exp;
branches;
next	1.25;

1.25
date	2002.01.18.14.04.03;	author wjv;	state Exp;
branches;
next	1.24;

1.24
date	2001.08.03.11.32.41;	author wjv;	state Exp;
branches;
next	1.23;

1.23
date	2001.06.27.10.14.47;	author wjv;	state Exp;
branches;
next	1.22;

1.22
date	2001.06.15.12.11.33;	author wjv;	state Exp;
branches;
next	1.21;

1.21
date	2001.05.30.14.34.48;	author kevlo;	state Exp;
branches;
next	1.20;

1.20
date	2001.05.07.12.18.57;	author jeh;	state Exp;
branches;
next	1.19;

1.19
date	2001.03.12.10.33.50;	author nbm;	state Exp;
branches;
next	1.18;

1.18
date	2001.02.28.15.58.11;	author kevlo;	state Exp;
branches;
next	1.17;

1.17
date	2001.02.20.15.51.29;	author kevlo;	state Exp;
branches;
next	1.16;

1.16
date	2001.02.12.10.01.01;	author knu;	state Exp;
branches;
next	1.15;

1.15
date	2001.01.29.15.47.57;	author kevlo;	state Exp;
branches;
next	1.14;

1.14
date	2001.01.24.11.36.35;	author kevlo;	state Exp;
branches;
next	1.13;

1.13
date	2000.12.04.13.00.07;	author roam;	state Exp;
branches;
next	1.12;

1.12
date	2000.11.28.01.43.39;	author jeh;	state Exp;
branches;
next	1.11;

1.11
date	2000.11.19.03.06.48;	author jeh;	state Exp;
branches;
next	1.10;

1.10
date	2000.11.13.13.48.48;	author jeh;	state Exp;
branches;
next	1.9;

1.9
date	2000.11.01.11.54.56;	author jeh;	state Exp;
branches;
next	1.8;

1.8
date	2000.11.01.11.49.07;	author jeh;	state Exp;
branches;
next	1.7;

1.7
date	2000.10.10.04.54.35;	author kevlo;	state Exp;
branches;
next	1.6;

1.6
date	2000.09.22.10.24.52;	author kris;	state Exp;
branches;
next	1.5;

1.5
date	2000.09.08.10.07.11;	author nbm;	state Exp;
branches;
next	1.4;

1.4
date	2000.09.07.14.02.51;	author nbm;	state Exp;
branches;
next	1.3;

1.3
date	2000.08.21.10.07.20;	author sobomax;	state Exp;
branches;
next	1.2;

1.2
date	2000.08.12.16.15.47;	author nbm;	state Exp;
branches;
next	1.1;

1.1
date	2000.07.31.19.13.53;	author nbm;	state Exp;
branches;
next	;


desc
@@


1.66
log
@Switch exporter over
@
text
@# Created by: Johann Visagie <johann@@egenetics.com>
# $FreeBSD: head/biology/emboss/Makefile 305131 2012-10-01 14:55:55Z wen $

PORTNAME=	emboss
PORTVERSION=	6.2.0
RELEASE=	${PORTNAME:U}-${PORTVERSION}
PORTREVISION=	2
CATEGORIES=	biology
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
DISTNAME=	${RELEASE}
DIST_SUBDIR=	${PORTNAME}

MAINTAINER=	wen@@FreeBSD.org
COMMENT=	A collection of open source tools for genetic sequence analysis

BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
		primer3:${PORTSDIR}/biology/primer3
LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
		png15:${PORTSDIR}/graphics/png

CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*

PREFIX?=	${LOCALBASE}/emboss
NO_MTREE=	yes
USE_SUBMAKE=	yes
USE_GMAKE=	yes
GNU_CONFIGURE=	yes
USE_AUTOTOOLS=	libtool
USE_LDCONFIG=	yes
USE_MOTIF=	yes
SUB_FILES=	pkg-message
SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}

DOCSDIR=	${PREFIX}/share/${PORTNAME:U}/doc
DATADIR=	${PREFIX}/share/${PORTNAME:U}

CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}

.if !defined(WITHOUT_X11)
USE_XORG=	x11
USE_MOTIF=	yes
LIB_DEPENDS+=	gd.4:${PORTSDIR}/graphics/gd \
		png15:${PORTSDIR}/graphics/png
.else
CONFIGURE_ARGS+= --without-x
.endif

DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template

pre-install:
	@@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}

post-install:
	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
	@@ ${CAT} ${PKGMESSAGE}

.include <bsd.port.mk>
@


1.65
log
@SVN rev 305131 on 2012-10-01 14:55:55Z by wen

- Take maintainership
@
text
@d2 1
a2 1
# $FreeBSD$
@


1.64
log
@SVN rev 305130 on 2012-10-01 14:45:16Z by tabthorpe

- Reassign to the heap at maintainer's request
@
text
@d13 1
a13 1
MAINTAINER=	ports@@FreeBSD.org
@


1.63
log
@- update png to 1.5.10
@
text
@d1 1
a1 4
# New ports collection makefile for:	emboss
# Date created:		31 July 2000
# Whom:	      		Johann Visagie <johann@@egenetics.com>
#
a2 1
#
d13 1
a13 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.62
log
@Bump PORTREVISION after open-mofit update
@
text
@d11 1
a11 1
PORTREVISION=	1
d23 1
a23 1
		png.6:${PORTSDIR}/graphics/png
d47 1
a47 1
		png.6:${PORTSDIR}/graphics/png
@


1.61
log
@Sync to new bsd.autotools.mk
@
text
@d11 1
@


1.60
log
@- Update to 6.2.0

Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)
@
text
@d31 1
a31 1
USE_AUTOTOOLS=	libtool:22
@


1.59
log
@- update to 1.4.1
Reviewed by:	exp8 run on pointyhat
Supported by:	miwi
@
text
@d9 1
a9 2
PORTVERSION=	6.0.1
PORTREVISION=	3
d12 1
a12 1
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/
@


1.58
log
@- update to jpeg-8
@
text
@d10 1
a10 1
PORTREVISION=	2
d23 1
a23 1
		png.5:${PORTSDIR}/graphics/png
d47 1
a47 1
		png.5:${PORTSDIR}/graphics/png
@


1.57
log
@- Update MASTER_SITES

PR:		137750
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d10 1
a10 1
PORTREVISION=	1
@


1.56
log
@-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:	marcus and kwm
Pointyhat-exp:	a few times by pav
Tested by:	pgollucci, "Romain Tartière" <romain@@blogreen.org>, and
		a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:	marcus
Approved by:	portmgr
@
text
@d13 1
a13 2
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
@


1.55
log
@- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated
Requested by:	edwin
@
text
@d33 1
a33 1
USE_AUTOTOOLS=	libtool:15
@


1.54
log
@- Force commit to correct the entry
- Update to 6.0.1

PR:		132504
Submitted by:	Wen Heping <wenheping@@gmail.com>
Approved by:	maintainer
@
text
@d10 1
@


1.53
log
@- Update to 0.1.24

PR:		132527
Submitted by:	Wen Heping <wenheping@@gmail.com>
Approved by:	maintainer
@
text
@@


1.52
log
@- Replace SF with second working master site

Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d9 1
a9 1
PORTVERSION=	5.0.0
@


1.51
log
@- It seems that upstream removes their distfiles from sourceforge, so add
  the download site pointed by their webpage as first choice.

Noticed by:    pointyhat via pav
@
text
@d13 1
a13 1
		SF
@


1.50
log
@- Update to 5.0.0

PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d12 2
a13 1
MASTER_SITES=	SF
@


1.49
log
@- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
@
text
@d9 2
a10 2
PORTVERSION=	3.0.0
PORTREVISION=	2
d12 2
a13 6
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTNAME=	${PORTNAME:U}-${PORTVERSION}
DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
d32 1
a32 1
INSTALLS_SHLIB=	yes
d37 1
a37 1
DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
d40 11
a53 9
post-patch:
.if !defined(NOPORTDOCS)
.for DIR in ${DOC_DIRS}
	@@ ${REINPLACE_CMD} -e \
	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
	  ${WRKSRC}/${DIR}/Makefile.in
.endfor
.endif

@


1.48
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@d10 1
a10 1
PORTREVISION=	1
a36 1
USE_XLIB=	yes
@


1.47
log
@For EMBOSS:

	This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
@
text
@d10 1
@


1.46
log
@Conversion to a single libtool environment.

Approved by:	portmgr (kris)
@
text
@d9 1
a9 2
PORTVERSION=	2.10.0
PORTREVISION=	1
d11 2
a12 1
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
d17 1
d27 1
a27 1
CONFLICTS=	qmail-ldap2-* digest-*
d29 2
d34 1
d38 2
a39 2
USE_REINPLACE=	yes
PKGMESSAGE=	${WRKDIR}/pkg-message
d50 1
a50 1
	${REINPLACE_CMD} -e \
d56 3
d60 1
a60 6
	@@ cd ${WRKSRC} && \
	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
	@@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
.if !defined(BATCH)
a61 1
.endif
@


1.45
log
@Remove CONFLICTS with nss.
@
text
@d10 1
a30 1
USE_AUTOTOOLS=	libtool:15
@


1.44
log
@Mass-conversion to the USE_AUTOTOOLS New World Order.  The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
	http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.
@
text
@d25 1
a25 1
CONFLICTS=	nss-* qmail-ldap2-* digest-*
@


1.43
log
@- Update to 2.10.0

PR:		ports/81579
Submitted by:	"Choe, Cheng-Dae" <whitekid@@gmail.com>
Approved by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d30 1
a30 1
USE_LIBTOOL_VER=15
@


1.42
log
@- Add (or fix) CONFLICTS line. The ports install bin/digest.

Approved by:	portmgr (krion)
@
text
@d9 1
a9 1
PORTVERSION=	2.9.0
@


1.41
log
@- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
@
text
@d25 2
@


1.40
log
@With portmgr hat on, reset inactive maintainer.
@
text
@d9 1
a9 2
PORTVERSION=	2.4.1
PORTREVISION=	3
d11 4
a14 3
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/old/ \
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/
#		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
a15 2
DIST_SUBDIR=	${PORTNAME}
EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
d17 1
a17 1
MAINTAINER=	ports@@FreeBSD.org
d20 4
a23 1
LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd
d28 1
d32 1
a32 1
USE_PERL5_BUILD=yes
d35 2
a36 3
.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
.endif
a37 13
CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include" \
		LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
		MKDIR="${MKDIR}" RM="${RM}"

WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
EMNU_VERSION=	1.0.5
HMMER_VERSION=	2.1.1
MEME_VERSION=	2.3.1
MSE_VERSION=	0.0.4
TOPO_VERSION=	0.1
PHYLIP_VERSION=	3.573c
a40 39
.for app in EMNU HMMER MEME MSE PHYLIP TOPO
SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
.if defined(WITH_${app})
APPLIST+=	${app}
${app}_WRKSRC=	${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
DISTFILES+=	${${app}_DISTFILE}
PLIST_${app}=	""
.else
PLIST_${app}=	"@@comment "
.endif
PLIST_SUB+=	PLIST_${app}=${PLIST_${app}}
.endfor

# Jemboss support is a work in progress.
#
#.if defined(WITH_JEMBOSS)
#USE_JAVA=	1.3+
#CONFIGURE_ARGS+=	--with-java=${JAVA_HOME}/include \
#			--with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
#CONFIGURE_ENV+=	PATH=${PATH}:${JAVA_HOME}/bin
#MAKE_ENV+=	PATH=${PATH}:${JAVA_HOME}/bin
#JEMBOSS_WRKSRC=	${WRKSRC}/jemboss
#.endif

pre-fetch:
	@@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}

post-extract:
.for app in ${APPLIST}
	@@ ${MKDIR} ${EMBASSY_WRKDIR}
	@@ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \
	  ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS}
	@@ if [ `id -u` = 0 ]; then \
	    ${CHMOD} -R ug-s ${${app}_WRKSRC}; \
	    ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
	  fi
.endfor

d42 1
d44 2
a45 2
	@@ ${PERL} -pi.orig -e \
	  's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
d48 1
a48 24

post-configure:
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
	  CXXFLAGS="${CXXFLAGS}" \
	  INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
	  INSTALL_DATA="${INSTALL_DATA}" \
	  INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
	  INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
	  ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.endfor

post-build:
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
	  ${MAKE_ARGS}
.endfor
#.if defined(WITH_JEMBOSS)
#	@@ cd ${JEMBOSS_WRKSRC} && \
#	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
#	  ${MAKE_ARGS}
#.endif
d51 5
a55 11
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
	  ${MAKE_ARGS} ${INSTALL_TARGET}
.endfor
	@@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
	  ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
	  ${CHOWN} ${SHAREOWN}:${SHAREGRP} \
	  ${PREFIX}/etc/emboss.default.sample
	@@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
	  pkg-message > ${PKGMESSAGE}
a59 3
post-clean:
	@@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc

@


1.39
log
@Fix MASTER_SITES:
 - add trailing slash
 - ftp.ebi.ac.uk only has 2.8.0

PR:		ports/67427
Submitted by:	Roman Neuhauser
Approved by:	maintainer timeout
@
text
@d19 1
a19 1
MAINTAINER=	wjv@@FreeBSD.org
@


1.38
log
@Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)
@
text
@d13 2
a14 2
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
@


1.37
log
@Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:	Oliver Eikemeier
@
text
@d10 1
a10 1
PORTREVISION=	2
@


1.36
log
@Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
@
text
@d30 1
a30 1
USE_PERL=	yes
@


1.35
log
@o Main modification
  graphics/gd(based on 1.8.4)    -> graphics/gd1
  graphics/gd2(based on 2.0.15)  -> graphics/gd
  graphics/p5-GD(based on 1.41)  -> graphics/p5-GD1
  graphics/p5-GD2(based on 2.07) -> graphics/p5-GD
  japanese/gd                    -> japanese/gd1
  japanese/gd2                   -> japanese/gd
o Include some feature
  WITH_XPM(w/, w/o WITHOUT_X11)
o Chase this modification
o Fix build error [1]

PR:		ports/54540
Submitted by:	Ports Fury
Approved by:	maintainer (blanket)
Reported by:	bento via kris [1]
@
text
@d30 1
@


1.34
log
@This port is scheduled for removal on Nov 7 2003 if it is still broken at
that time and no PRs have been submitted to fix it.  If you are interested
in saving this port, please send your patches to the maintainer.  If the
maintainer is unresponsive or the port has no maintainer, then please
submit them via send-pr.
@
text
@d10 1
a10 1
PORTREVISION=	1
d13 1
a13 1
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
d22 1
a22 3
BROKEN=		Checksum mismatch

LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd2
d36 1
a36 1
CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
@


1.33
log
@BROKEN: Checksum mismatch
@
text
@@


1.32
log
@o Change library name from libgd to libgd1.
o Do not install everything except headers and libraries
  (to avoid conflicting with graphics/gd2)
o Fix dependency on new libgd1(for many ports).

PR:		ports/54100
Submitted by:	Ports Fury
@
text
@d22 2
@


1.31
log
@Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
@
text
@d10 1
d22 1
a22 1
LIB_DEPENDS=	gd.2:${PORTSDIR}/graphics/gd
@


1.30
log
@- Unbreak fetching of distfiles.  (Needs update as soon as freeze is over.)

Submitted by:	kris, bento
Approved by:	Implicitly by first rule of ports freeze, I hope!
@
text
@d19 1
@


1.29
log
@BROKEN: Does not fetch
@
text
@d11 1
a11 1
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
a18 2

BROKEN=		"Does not fetch"
@


1.28
log
@- Update to version 2.4.1
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)

PR:		40198 ; many private requests
Submitted by:	Tilman Linneweh <tilman@@arved.de> (2.4.1 update)
@
text
@d20 2
@


1.27
log
@BROKEN: incorrect checksums
@
text
@d9 1
a9 1
PORTVERSION=	2.2.0
a21 2
BROKEN=		"Incorrect checksums"

d64 11
d98 1
a98 1
	@@ (cd ${${app}_WRKSRC} && \
d105 1
a105 1
	  ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
d110 1
a110 1
	@@ (cd ${${app}_WRKSRC} && \
d112 1
a112 1
	  ${MAKE_ARGS})
d114 5
d122 1
a122 1
	@@ (cd ${${app}_WRKSRC} && \
d124 1
a124 1
	  ${MAKE_ARGS} ${INSTALL_TARGET})
@


1.26
log
@Add USE_SUBMAKE, where it might be necessary.
@
text
@d22 2
@


1.25
log
@- Update to version 2.2.0
- Update included EMBASSY package EMNU
- Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from
  being generated properly
- Consider this an interim update merely to track the latest version - more
  work is required to activate the newly included "Jemboss" Java GUI
  interface
@
text
@d22 1
@


1.24
log
@- Update port to version 2.0.1
- Add two new EMBASSY applications, MEME and HMMER.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.23 2001/06/27 10:14:47 wjv Exp $
d9 1
a9 1
PORTVERSION=	2.0.1
a11 1
		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
d23 1
a23 1
USE_LIBTOOL=	yes
d40 1
a40 1
EMNU_VERSION=	1.0.4
a112 1
.if !defined(BATCH)
d115 1
@


1.23
log
@Updating my email address in my remaining ports.

Prompted by:	vanilla
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.22 2001/06/15 12:11:33 wjv Exp $
d9 1
a9 1
PORTVERSION=	1.13.3
d25 1
d42 2
d50 1
a50 1
.for app in EMNU MSE PHYLIP TOPO
@


1.22
log
@Update to 1.13.3; remove bogus file.

PR:		28119
Reviewed by:	nbm
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.21 2001/05/30 14:34:48 kevlo Exp $
d19 1
a19 1
MAINTAINER=	johann@@egenetics.com
@


1.21
log
@Update to version 1.13.1

PR: 27768
Submitted by: MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.20 2001/05/07 12:18:57 jeh Exp $
d9 1
a9 1
PORTVERSION=	1.13.1
@


1.20
log
@Update the EMBOSS suite (biology/emboss) to version 1.12.0

PR:		27179
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.19 2001/03/12 10:33:50 nbm Exp $
d9 1
a9 1
PORTVERSION=	1.12.0
d45 1
d108 1
a108 2
	  ${WRKSRC}/emboss/acd/emboss.default > \
	  ${PREFIX}/etc/emboss.default.sample && \
@


1.19
log
@Update the EMBOSS suite to v1.11.0

PR:		25728
Submitted by:	johann@@egenetics.com
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.18 2001/02/28 15:58:11 kevlo Exp $
d9 1
a9 1
PORTVERSION=	1.11.0
@


1.18
log
@Update to version 1.10.1

PR: 25449
Submitted by: maintainer
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.17 2001/02/20 15:51:29 kevlo Exp $
d9 1
a9 1
PORTVERSION=	1.10.1
d21 1
a21 2
LIB_DEPENDS=	gd.2:${PORTSDIR}/graphics/gd \
		png.4:${PORTSDIR}/graphics/png
@


1.17
log
@Update to version 1.10.0

PR: 25228
Submitted by: MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.16 2001/02/12 10:01:01 knu Exp $
d9 1
a9 1
PORTVERSION=	1.10.0
@


1.16
log
@Chase graphics/gd's shlib version bump.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.15 2001/01/29 15:47:57 kevlo Exp $
d9 1
a9 2
PORTVERSION=	1.9.1
PORTREVISION=	1
d41 1
a41 1
EMNU_VERSION=	1.0.3
d107 4
a110 1
	@@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
@


1.15
log
@- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1
- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one

PR: 24717
Submitted by: MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.14 2001/01/24 11:36:35 kevlo Exp $
d10 1
d22 1
a22 1
LIB_DEPENDS=	gd.1:${PORTSDIR}/graphics/gd \
@


1.14
log
@Upgrade to version 1.9.0

PR: 24597
Submitted by: MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.13 2000/12/04 13:00:07 roam Exp $
d9 1
a9 1
PORTVERSION=	1.9.0
d13 1
a27 1
PLIST=		${WRKDIR}/pkg-plist
a35 1

d37 1
a37 2
		MKDIR="${MKDIR}" \
		RM="${RM}"
d41 1
a41 1
EMNU_VERSION=	1.0.2
d45 2
a50 1
PLISTS+=	${PKGDIR}/pkg-plist.${app}
d54 3
d58 1
a59 2
PLISTS+=	${PKGDIR}/pkg-plist
DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
d78 1
a78 1
	  "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
a99 3

pre-install:
	@@ ${CAT} ${PLISTS} > ${PLIST}
@


1.13
log
@Update distfiles' checksums after the distfiles have been rerolled yet
again without changing names or versions.  Also add a new MASTER_SITE.

PR:		23262
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.12 2000/11/28 01:43:39 jeh Exp $
d9 1
a9 1
PORTVERSION=	1.8.0
d26 1
d35 1
a35 1
		LIBS="-L${LOCALBASE}/lib"
d43 1
a43 1
PHYLIP_VERSION=	3.573c
d46 2
a47 1
.for app in MSE PHYLIP TOPO
@


1.12
log
@- Update port biology/emboss from 1.7.0 to 1.8.0

PR:		23130
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.11 2000/11/19 03:06:48 jeh Exp $
d12 2
a13 1
		ftp://ftp.no.embnet.org/pub/EMBOSS/
@


1.11
log
@Make nolonger support :U.  Fix to compensate for that.

Submitted by:	fenner
Approved by:	MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.10 2000/11/13 13:48:48 jeh Exp $
d9 1
a9 2
PORTVERSION=	1.7.0
PORTREVISION=	1
d13 1
a13 1
DISTFILES=	${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX}
d15 1
a15 1
EXTRACT_ONLY=	${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX}
d26 1
a26 3

# Make doesn't know about :U
PORTNAME_U=	EMBOSS
d39 1
a39 1
WRKSRC=		${WRKDIR}/${PORTNAME_U}-${PORTVERSION}
d109 2
@


1.10
log
@- This is a fairly extensive rework of this port.
- "EMBASSY" applications are third party tools which have been adapted to
  function as part of EMBOSS, but which are not included with the base EMBOSS
  distribution for licensing or other reasons.  This new version of the
  EMBOSS port now contains the three current EMBASSY applications as well,
  and during installation the user is presented with a dialog(1) menu to
  choose which of these should be isntalled.

PR:		22818
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.9 2000/11/01 11:54:56 jeh Exp $
d14 1
a14 1
DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
d16 1
a16 1
EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
d28 3
d42 1
a42 1
WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
@


1.9
log
@Make portlint happy, remove a space
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.8 2000/11/01 11:49:07 jeh Exp $
d10 1
d14 3
a16 1
DISTNAME=	EMBOSS-${PORTVERSION}
d26 1
d28 5
a32 1
CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
d35 20
d57 14
d78 22
d101 5
d111 3
@


1.8
log
@Update to version 1.7.0

PR:		22474
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.7 2000/10/10 04:54:35 kevlo Exp $
d27 1
a27 1
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
@


1.7
log
@- Update to 1.6.0
- Reorder packing list

PR: 21857
Submitted by: MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.6 2000/09/22 10:24:52 kris Exp $
d9 1
a9 1
PORTVERSION=	1.6.0
@


1.6
log
@Add USE_XLIB
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.5 2000/09/08 10:07:11 nbm Exp $
d9 1
a9 1
PORTVERSION=	1.5.0
@


1.5
log
@Upgrade to 1.5.0

PR:		21108
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.4 2000/09/07 14:02:51 nbm Exp $
d22 1
@


1.4
log
@Update to emboss 1.4.0.

PR:		ports/20898
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.3 2000/08/21 10:07:20 sobomax Exp $
d9 1
a9 1
PORTVERSION=	1.4.0
d11 2
a12 1
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/
@


1.3
log
@USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.2 2000/08/12 16:15:47 nbm Exp $
d9 1
a9 1
PORTVERSION=	1.1.0
d25 9
a39 9

DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html

post-patch:
.for DIR in ${DOC_DIRS}
	@@perl -pi.orig -e \
		"s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
		${WRKSRC}/${DIR}/Makefile.in
.endfor
@


1.2
log
@Update to emboss 1.1.0, fixing some style bugs too.

PR:		ports/20519
Submitted by:	Johann Visagie <johann@@egenetics.com> (maintainer)
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/emboss/Makefile,v 1.1 2000/07/31 19:13:53 nbm Exp $
a19 1
GNU_CONFIGURE=	yes
@


1.1
log
@Add emboss, the European Molecular Biology Open Software Suite

PR:		ports/20317
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d5 1
a5 1
# $FreeBSD$
d9 1
a9 1
PORTVERSION=	1.0.0
d25 16
@

