head	1.24;
access;
symbols
	RELEASE_8_3_0:1.19
	RELEASE_9_0_0:1.19
	RELEASE_7_4_0:1.17
	RELEASE_8_2_0:1.17
	RELEASE_6_EOL:1.17
	RELEASE_8_1_0:1.17
	RELEASE_7_3_0:1.15
	RELEASE_8_0_0:1.14
	RELEASE_7_2_0:1.11
	RELEASE_7_1_0:1.10
	RELEASE_6_4_0:1.10
	RELEASE_5_EOL:1.10
	RELEASE_7_0_0:1.8
	RELEASE_6_3_0:1.8
	PRE_XORG_7:1.7
	RELEASE_4_EOL:1.6
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	RELEASE_5_4_0:1.3
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comment	@# @;


1.24
date	2013.03.19.15.34.37;	author svnexp;	state Exp;
branches;
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1.23
date	2012.11.17.05.54.51;	author svnexp;	state Exp;
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1.22
date	2012.10.01.14.55.55;	author wen;	state Exp;
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1.21
date	2012.10.01.14.45.16;	author tabthorpe;	state Exp;
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1.20
date	2012.06.01.05.16.28;	author dinoex;	state Exp;
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1.19
date	2011.09.23.22.21.21;	author amdmi3;	state Exp;
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1.18
date	2011.05.02.12.44.26;	author makc;	state Exp;
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1.17
date	2010.04.07.01.21.36;	author wen;	state Exp;
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1.16
date	2010.03.28.06.31.36;	author dinoex;	state Exp;
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1.15
date	2010.02.05.11.34.36;	author dinoex;	state Exp;
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1.14
date	2009.08.14.08.33.22;	author miwi;	state Exp;
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1.13
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1.10
date	2008.04.13.07.22.42;	author rafan;	state Exp;
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1.9
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1.1
date	2004.11.26.16.34.22;	author sem;	state Exp;
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desc
@@


1.24
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/314609
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@# Created by: Fernan Aguero <fernan@@iib.unsamn.edu.ar>
# $FreeBSD: head/biology/embassy/Makefile 314609 2013-03-18 23:35:01Z jgh $

PORTNAME=	embassy
PORTVERSION=	6.2.0
PORTREVISION=	2
CATEGORIES=	biology
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
DIST_SUBDIR=	emboss

MAINTAINER=	wen@@FreeBSD.org
COMMENT=	Collection of contributed EMBOSS applications

LIB_DEPENDS=	nucleus.6:${PORTSDIR}/biology/emboss

PREFIX?=	${LOCALBASE}/emboss
NO_MTREE=	yes
USE_SUBMAKE=	yes
USE_ICONV=	yes
USE_GMAKE=	yes
GNU_CONFIGURE=	yes
USE_XORG=	x11
USE_MOTIF=	yes
USE_LDCONFIG=	yes

OPTIONS_DEFINE=	DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \
		EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \
		VIENNA MIRA IPRSCAN CBSTOOLS

DOMAINATRIX_DESC=	Protein domain apps
DOMALIGN_DESC=	Protein domain apps
DOMSEARCH_DESC=	Protein domain apps
SIGNATURE_DESC=	Protein domain apps
STRUCTURE_DESC=	Protein domain apps
EMNU_DESC=	EMBOSS simple menu
ESIM4_DESC=	Align cDNA/EST to genome
HMMER_DESC=	HMM alignment and searches
MEMENEW_DESC=	Motif detection
MSE_DESC=	A multiple sequence screen editor
MYEMBOSS_DESC=	Examples for developers of EMBOSS apps
PHYLIPNEW_DESC=	Phylogeny inference
TOPO_DESC=	Transmembrane display
VIENNA_DESC=	RNA folding
MIRA_DESC=	Whole Genome shotgun and EST assembler
IPRSCAN_DESC=	InterPro scan
CBSTOOLS_DESC=	CBS Tools

OPTIONS_DEFAULT=	DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \
		EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \
		VIENNA MIRA IPRSCAN CBSTOOLS

CPPFLAGS+=	-I${PREFIX}/include -I${LOCALBASE}/include -I${LOCALBASE}/emboss/include
LDFLAGS+=	-L${PREFIX}/lib -L${LOCALBASE}/lib -L${LOCALBASE}/emboss/lib

CONFIGURE_ENV=	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}"

EMBASSY_WRKDIR=		${WRKSRC}/EMBASSY
DOMAINATRIX_VERSION=	0.1.0
EMNU_VERSION=		1.05
ESIM4_VERSION=		1.0.0
HMMER_VERSION=		2.3.2
MEMENEW_VERSION=	4.0.0
MSE_VERSION=		3.0.0
TOPO_VERSION=		2.0.0
PHYLIPNEW_VERSION=	3.69
DOMALIGN_VERSION=	0.1.0
DOMSEARCH_VERSION=	0.1.0
SIGNATURE_VERSION=	0.1.0
STRUCTURE_VERSION=	0.1.0
MYEMBOSS_VERSION=	6.2.0
VIENNA_VERSION=		1.7.2
MIRA_VERSION=		2.8.2
IPRSCAN_VERSION=	4.3.1
CBSTOOLS_VERSION=	1.0.0
EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEMENEW MSE PHYLIPNEW \
			TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \
			VIENNA MIRA IPRSCAN CBSTOOLS

.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>

.for app in ${EMBASSY_APPS}
.if ${PORT_OPTIONS:M${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

do-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

post-extract:
	@@${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in

post-patch:
	@@${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|'

do-configure:
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.endfor

do-build:
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS}
.endfor

do-install:
.for app in ${APPLIST}
	@@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
	  ${MAKE_ARGS} ${INSTALL_TARGET}
.endfor

.include <bsd.port.post.mk>
@


1.23
log
@Switch exporter over
@
text
@d2 1
a2 1
# $FreeBSD: head/biology/embassy/Makefile 305131 2012-10-01 14:55:55Z wen $
d12 1
a12 1
COMMENT=	A collection of contributed EMBOSS applications
d26 25
a50 17
OPTIONS=	DOMAINATRIX	"Protein domain apps" on \
		DOMALIGN	"Protein domain apps" on \
		DOMSEARCH	"Protein domain apps" on \
		SIGNATURE	"Protein domain apps" on \
		STRUCTURE	"Protein domain apps" on \
		EMNU		"EMBOSS simple menu" on \
		ESIM4		"Align cDNA/EST to genome" on \
		HMMER		"HMM alignment and searches" on \
		MEMENEW		"Motif detection" on \
		MSE		"A multiple sequence screen editor" on \
		MYEMBOSS	"Examples for developers of EMBOSS apps" on \
		PHYLIPNEW	"Phylogeny inference" on \
		TOPO		"Transmembrane display" on \
		VIENNA		"RNA folding" on \
		MIRA		"Whole Genome shotgun and EST assembler" on \
		IPRSCAN		"InterPro scan" on \
		CBSTOOLS	"CBS Tools" on
d80 1
d83 1
a83 1
.if !defined(WITHOUT_${app})
@


1.22
log
@SVN rev 305131 on 2012-10-01 14:55:55Z by wen

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


1.21
log
@SVN rev 305130 on 2012-10-01 14:45:16Z by tabthorpe

- Reassign to the heap at maintainer's request
@
text
@d11 1
a11 1
MAINTAINER=	ports@@FreeBSD.org
@


1.20
log
@- update png to 1.5.10
@
text
@d1 1
a1 5
# ex:ts=8
# New ports collection makefile for:	embassy
# Date created:		1.November.2004
# Whom:	      		Fernan Aguero <fernan@@iib.unsamn.edu.ar>
#
a2 1
#
d11 1
a11 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.19
log
@- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:		157936
Submitted by:	myself
Exp-runs by:	pav
Approved by:	pav
@
text
@d11 1
a11 1
PORTREVISION=	1
@


1.18
log
@Bump PORTREVISION after open-mofit update
@
text
@d49 4
a52 2
CONFIGURE_ENV+=	CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include -I${LOCALBASE}/emboss/include" \
		LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib -L${LOCALBASE}/emboss/lib"
@


1.17
log
@- Update to 6.2.0

Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)
@
text
@d11 1
@


1.16
log
@- update to 1.4.1
Reviewed by:	exp8 run on pointyhat
Supported by:	miwi
@
text
@d10 1
a10 2
PORTVERSION=	6.0.0
PORTREVISION=	3
d12 1
a12 1
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/
d56 4
a59 4
MEMENEW_VERSION=	0.1.0
MSE_VERSION=		1.0.0
TOPO_VERSION=		1.0.0
PHYLIPNEW_VERSION=	3.67
d64 1
a64 1
MYEMBOSS_VERSION=	6.0.0
d99 3
@


1.15
log
@- update to jpeg-8
@
text
@d11 1
a11 1
PORTREVISION=	2
@


1.14
log
@- Update MASTER_SITES

PR:		137750
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d11 1
a11 1
PORTREVISION=	1
@


1.13
log
@- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated
Requested by:	edwin
@
text
@d13 1
a13 2
MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
@


1.12
log
@- Update to 6.0.0
- Unbreak

PR:		135376
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d11 1
@


1.11
log
@- Mark BROKEN does not compile

Submitted by:	maintainer via private mail
@
text
@d10 1
a10 1
PORTVERSION=	5.0.0
d19 1
a19 3
LIB_DEPENDS=	nucleus.5:${PORTSDIR}/biology/emboss

BROKEN=		does not compile
d39 1
a39 1
		MEME		"Motif detection" on \
d42 1
a42 1
		PHYLIP		"Phylogeny inference" on \
d44 4
a47 1
		VIENNA		"RNA folding" on
d49 2
a50 2
CONFIGURE_ENV+=	CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
		LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
d57 1
a57 1
MEME_VERSION=		0.1.0
d60 1
a60 1
PHYLIP_VERSION=		3.6b
d65 6
a70 3
MYEMBOSS_VERSION=	3.0.0
VIENNA_VERSION=		1.6
EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP \
d72 1
a72 1
			VIENNA
@


1.10
log
@- Update to 5.0.0

PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d21 2
@


1.9
log
@- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:	portmgr (xorg cleanup)
@
text
@d10 1
a10 2
PORTVERSION=	3.0.0
PORTREVISION=	2
a12 2
		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
d19 1
a19 1
LIB_DEPENDS=	nucleus.3:${PORTSDIR}/biology/emboss
d27 1
d29 1
d43 2
a44 1
		TOPO		"Transmembrane display" on
d53 2
a54 2
HMMER_VERSION=		2.1.1
MEME_VERSION=		2.3.1
d63 4
a66 2
EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \
			DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS
@


1.8
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@d11 1
a11 1
PORTREVISION=	1
a29 1
USE_XLIB=	yes
@


1.7
log
@- Fix after objformat removal

Reported by:	pointyhat
@
text
@d11 1
@


1.6
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
@d92 3
@


1.5
log
@Add missing USE_ICONV
@
text
@d10 1
a10 1
PORTVERSION=	2.10.0
d12 2
a13 1
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
d16 1
a16 1
DIST_SUBDIR=	${PORTNAME}
d21 1
a21 1
LIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss
d23 2
d32 5
a36 1
OPTIONS=	DOMAINATRIX	"Protein structure and domain apps" on \
d42 1
d50 1
a50 1
DOMAINATRIX_VERSION=	1.0.0
d57 8
a64 2
PHYLIP_VERSION=		3.57c
EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO
a91 10
.if !defined(WITHOUT_DOMAINATRIX)
pre-configure::
	@@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/domainatrix-patch-Makefile.in
.endif

.if !defined(WITHOUT_EMNU)
pre-configure::
	@@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/emnu-patch-Makefile.in
.endif

@


1.4
log
@- Update to 2.10.0

Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d23 1
@


1.3
log
@- Fix OPTIONS handling

Pointy hat to:	sem
@
text
@d1 1
d10 1
a10 1
PORTVERSION=	2.9.0
d20 1
a20 2
BUILD_DEPENDS=	${LOCALBASE}/include/emboss.h:${PORTSDIR}/biology/emboss
LIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss:install
d33 1
a33 1
		MSE		"Sequence editor" on \
d77 10
@


1.2
log
@BROKEN: Broken distinfo file
@
text
@a21 2
BROKEN=		Broken distinfo file

d54 1
a54 1
.if defined(WITH_${app})
@


1.1
log
@[new port] biology/embassy

PR:		ports/74330
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
@
text
@d22 2
@

