4 files changed, 150 insertions, 5 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 651c403ee3eb..5ffa3f400065 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -7,10 +7,13 @@
 
 PORTNAME=	emboss
 PORTVERSION=	1.7.0
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/
-DISTNAME=	EMBOSS-${PORTVERSION}
+DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
+DIST_SUBDIR=	${PORTNAME}
+EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 
 MAINTAINER=	johann@egenetics.com
 
@@ -20,12 +23,51 @@ LIB_DEPENDS=	gd.1:${PORTSDIR}/graphics/gd \
 USE_GMAKE=	yes
 USE_LIBTOOL=	yes
 USE_XLIB=	yes
+PLIST=		${WRKDIR}/pkg-plist
 
-CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
+.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
+.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
+.endif
+
+CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
 		LIBS="-L${LOCALBASE}/lib"
 
+SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
+		MKDIR="${MKDIR}" \
+		RM="${RM}"
+
+WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
+EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
+PHYLIP_VERSION=	3.573c
+MSE_VERSION=	0.0.4
+TOPO_VERSION=	0.1
+.for app in MSE PHYLIP TOPO
+SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
+.if defined(WITH_${app})
+APPLIST+=	${app}
+PLISTS+=	${PKGDIR}/pkg-plist.${app}
+${app}_WRKSRC=	${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
+${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
+DISTFILES+=	${${app}_DISTFILE}
+.endif
+.endfor
+PLISTS+=	${PKGDIR}/pkg-plist
 DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
 
+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:
 .for DIR in ${DOC_DIRS}
 	@ ${PERL} -pi.orig -e \
@@ -33,11 +75,41 @@ post-patch:
 	  ${WRKSRC}/${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
+
+pre-install:
+	@ ${CAT} ${PLISTS} > ${PLIST}
+
 post-install:
+.for app in ${APPLIST}
+	@ (cd ${${app}_WRKSRC} && \
+	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
+	  ${MAKE_ARGS} ${INSTALL_TARGET})
+.endfor
 	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
 	  ${PREFIX}/etc/emboss.default.sample
 .if !defined(BATCH)
 	@ ${CAT} ${PKGMESSAGE}
 .endif
 
+post-clean:
+	@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc
+
 .include <bsd.port.mk>
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index f2d8f7e3d2ef..72b54429db4b 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1 +1,4 @@
-MD5 (EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341
+MD5 (emboss/EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = e41b0552196e9b7b46ca0e9563e9384a
+MD5 (emboss/MSE-0.0.4.tar.gz) = 6ba124ff85465be3541d2e250248cd3d
+MD5 (emboss/TOPO-0.1.tar.gz) = 687c6ca8ba945520b11058ba28ee880d
diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr
index 3b212c44b033..37865f30eebe 100644
--- a/biology/emboss/pkg-descr
+++ b/biology/emboss/pkg-descr
@@ -4,12 +4,21 @@ analysis.  EMBOSS is produced by the European Molecular Biology Network
 (EMBnet - http://www.embnet.org/).
 
 All EMBOSS tools are all built around the same set of core libraries - AJAX
-and NUCLEUS - and therefore share a unified user interface and a uniform
-sequence addressing methodology.
+and NUCLEUS - and therefore share a unified user interface, have similar
+"look and feel", and implement a uniform sequence addressing methodology.
 
 The various components of EMBOSS are distributed under the GPL, except the
 core libraries which are under the LGPL.
 
+EMBASSY packages are third party applications which have been integrated with
+the EMBOSS suite, but which are not included in the base EMBOSS distribution
+for licensing or other reasons.  This port includes the three currently
+available EMBASSY applications - MSE, PHYLIP and TOPO.  During an interactive
+install the user will be asked to choose which of these will be installed
+(default: all).  Note that the EMBASSY version of PHYLIP should not clash
+with the standalone Phylip application due to the fact that its binaries have
+been renamed.
+
 WWW: http://www.uk.embnet.org/Software/EMBOSS/
 
 -- Johann Visagie <johann@egenetics.com>
diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss
new file mode 100644
index 000000000000..a17b495c50b1
--- /dev/null
+++ b/biology/emboss/scripts/configure.emboss
@@ -0,0 +1,61 @@
+#!/bin/sh
+
+if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
+  exit
+fi
+
+if [ "${BATCH}" ]; then
+  set \"MSE\" \"PHYLIP\" \"TOPO\"
+else
+  /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
+  --checklist "\n\
+These third party applications have been adapted to
+function as part of EMBOSS.\n
+Please select EMBASSY applications to install:" -1 -1 3 \
+MSE	"v${MSE_VERSION} - Phylogeny inference" ON \
+PHYLIP	"v${PHYLIP_VERSION} - Sequence editor" ON \
+TOPO	"v${TOPO_VERSION} - Transmembrane display" ON \
+2> /tmp/checklist.tmp.$$
+
+  retval=$?
+
+  if [ -s /tmp/checklist.tmp.$$ ]; then
+    set `cat /tmp/checklist.tmp.$$`
+  fi
+  ${RM} -f /tmp/checklist.tmp.$$
+
+  case $retval in
+    0)
+      if [ -z "$*" ]; then
+        echo "Nothing selected"
+      fi
+    ;;
+    1)
+      echo "Cancel pressed."
+      exit 1
+    ;;
+  esac
+fi
+
+${MKDIR} ${WRKDIRPREFIX}${CURDIR}
+exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
+
+while [ "$1" ]; do
+  case $1 in
+    \"MSE\")
+      echo "WITH_MSE=	yes"
+    ;;
+    \"PHYLIP\")
+      echo "WITH_PHYLIP=	yes"
+    ;;
+    \"TOPO\")
+      echo "WITH_TOPO=	yes"
+    ;;
+    *)
+      echo "Invalid option(s): $*" > /dev/stderr
+      ${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
+      exit 1
+    ;;
+  esac
+  shift
+done