- 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

4 files changed, 150 insertions, 5 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 651c403..5ffa3f4 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 f2d8f7e..72b5442 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 3b212c4..37865f3 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 0000000..a17b495
--- /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