- Update to 2.9.0

- Pass maintainership to submitter

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

1 files changed, 23 insertions, 105 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index c7d8b55f1fd9..18ad062199d2 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,137 +6,55 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	2.4.1
-PORTREVISION=	3
+PORTVERSION=	2.9.0
 CATEGORIES=	biology
-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/
+MASTER_SITES=	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}
-DIST_SUBDIR=	${PORTNAME}
-EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of open source tools for genetic sequence analysis
 
-LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd
+BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
+		primer3:${PORTSDIR}/biology/primer3
+LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
+		png.5:${PORTSDIR}/graphics/png
 
 USE_SUBMAKE=	yes
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
+USE_LIBTOOL_VER=15
 INSTALLS_SHLIB=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
-USE_PERL5_BUILD=yes
+USE_REINPLACE=	yes
 PKGMESSAGE=	${WRKDIR}/pkg-message
 
-.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
-.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
-.endif
-
-CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include" \
-		LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
-SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
-		MKDIR="${MKDIR}" RM="${RM}"
+DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
+DATADIR=	${PREFIX}/share/${PORTNAME:U}
 
-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
 DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
 CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
 
-.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
-
 post-patch:
+.if !defined(NOPORTDOCS)
 .for DIR in ${DOC_DIRS}
-	@ ${PERL} -pi.orig -e \
-	  's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
+	${REINPLACE_CMD} -e \
+	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
 	  ${WRKSRC}/${DIR}/Makefile.in
 .endfor
-
-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
+.endif
 
 post-install:
-.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}
+	@ 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)
 	@ ${CAT} ${PKGMESSAGE}
 .endif
 
-post-clean:
-	@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc
-
 .include <bsd.port.mk>