- 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

10 files changed, 118 insertions, 77 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 23e0b1f66e36..5d97534f4eb3 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,10 +6,11 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.9.0
+PORTVERSION=	1.9.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
+		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
 DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 DIST_SUBDIR=	${PORTNAME}
@@ -24,7 +25,6 @@ USE_GMAKE=	yes
 USE_LIBTOOL=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
-PLIST=		${WRKDIR}/pkg-plist
 PKGMESSAGE=	${WRKDIR}/pkg-message
 
 .if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
@@ -33,29 +33,30 @@ PKGMESSAGE=	${WRKDIR}/pkg-message
 
 CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
 		LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
-
 SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
-		MKDIR="${MKDIR}" \
-		RM="${RM}"
+		MKDIR="${MKDIR}" RM="${RM}"
 
 WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
 EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
-EMNU_VERSION=	1.0.2
+EMNU_VERSION=	1.0.3
 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
+
 .for app in EMNU 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}
+PLIST_${app}=	""
+.else
+PLIST_${app}=	"@comment "
 .endif
+PLIST_SUB+=	PLIST_${app}=${PLIST_${app}}
 .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}
@@ -74,7 +75,7 @@ post-extract:
 post-patch:
 .for DIR in ${DOC_DIRS}
 	@ ${PERL} -pi.orig -e \
-	  "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
+	  's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
 	  ${WRKSRC}/${DIR}/Makefile.in
 .endfor
 
@@ -97,9 +98,6 @@ post-build:
 	  ${MAKE_ARGS})
 .endfor
 
-pre-install:
-	@ ${CAT} ${PLISTS} > ${PLIST}
-
 post-install:
 .for app in ${APPLIST}
 	@ (cd ${${app}_WRKSRC} && \
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index fce228f6c4c0..c4a6dc2e7ca1 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,5 +1,5 @@
-MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c
-MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b
-MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3
-MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29
+MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9
+MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678
+MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f
+MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834
diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa
index f4b1bc46f7a1..d8bdbf96f9fb 100644
--- a/biology/emboss/files/patch-aa
+++ b/biology/emboss/files/patch-aa
@@ -17,7 +17,7 @@ The port installs ${PREFIX}/etc/emboss.default.sample
 +    if (!prefixRootFile)
 +    {
 +      ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
-+		   namInstallRoot, prefixCap, prefix);
++		   namInstallRoot, prefix);
 +      prefixRootFile = fopen (ajStrStr(namRootStr), "r");
 +    }
 +
diff --git a/biology/emboss/files/patch-configure b/biology/emboss/files/patch-configure
new file mode 100644
index 000000000000..da46a3c60faa
--- /dev/null
+++ b/biology/emboss/files/patch-configure
@@ -0,0 +1,11 @@
+--- configure.orig	Mon Jan 22 23:28:17 2001
++++ configure	Thu Jan 25 19:07:33 2001
+@@ -1473,7 +1473,7 @@
+ 
+ 
+ 
+-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
++AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
+ 
+ #AC_PROG_CXX
+ for ac_prog in mawk gawk nawk awk
diff --git a/biology/emboss/files/patch-emboss-acd-emboss.default b/biology/emboss/files/patch-emboss-acd-emboss.default
new file mode 100644
index 000000000000..8311f5b23837
--- /dev/null
+++ b/biology/emboss/files/patch-emboss-acd-emboss.default
@@ -0,0 +1,32 @@
+--- emboss/acd/emboss.default.orig	Mon Jan 22 23:26:54 2001
++++ emboss/acd/emboss.default	Mon Jan 29 16:23:15 2001
+@@ -1,9 +1,26 @@
+-SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
++#####################################################
++### Configuration options for FreeBSD EMBOSS port ###
++#####################################################
+ 
+-# Logfile - set this to a file that any user can append to
+-# and EMBOSS applications will automatically write log information
++# This is the compiled-in default.  Change only if
++# you know what you're doing!
++#
++#SET emboss_data /usr/local/share/EMBOSS/data
+ 
++# This is where your local databases reside
++# (this will differ from site to site):
++#
++SET emboss_tempdata /var/db/bio
++
++# Logfile - set this to a file that any user can append to and EMBOSS
++# applications will automatically write log information
++#
+ #SET emboss_logfile /packages/emboss/emboss/log
++
++
++###########################################
++### Configuration options for databases ###
++###########################################
+ 
+ # swissprot (Puffer fish entries)
+ # =========
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 1cba313f1bd0..426f0514ed51 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -1,3 +1,61 @@
+%%PLIST_EMNU%%bin/emnu
+%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_MSE%%bin/mse
+%%PLIST_MSE%%lib/libckit.a
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_PHYLIP%%bin/eclique
+%%PLIST_PHYLIP%%bin/econsense
+%%PLIST_PHYLIP%%bin/econtml
+%%PLIST_PHYLIP%%bin/econtrast
+%%PLIST_PHYLIP%%bin/ednacomp
+%%PLIST_PHYLIP%%bin/ednadist
+%%PLIST_PHYLIP%%bin/ednainvar
+%%PLIST_PHYLIP%%bin/ednaml
+%%PLIST_PHYLIP%%bin/ednamlk
+%%PLIST_PHYLIP%%bin/ednapars
+%%PLIST_PHYLIP%%bin/ednapenny
+%%PLIST_PHYLIP%%bin/edollop
+%%PLIST_PHYLIP%%bin/edolpenny
+%%PLIST_PHYLIP%%bin/efactor
+%%PLIST_PHYLIP%%bin/efitch
+%%PLIST_PHYLIP%%bin/egendist
+%%PLIST_PHYLIP%%bin/ekitsch
+%%PLIST_PHYLIP%%bin/emix
+%%PLIST_PHYLIP%%bin/eneighbor
+%%PLIST_PHYLIP%%bin/epenny
+%%PLIST_PHYLIP%%bin/eprotdist
+%%PLIST_PHYLIP%%bin/eprotpars
+%%PLIST_PHYLIP%%bin/erestml
+%%PLIST_PHYLIP%%bin/eseqboot
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
+%%PLIST_TOPO%%bin/topo
+%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
 bin/abiview
 bin/acdc
 bin/antigenic
diff --git a/biology/emboss/pkg-plist.EMNU b/biology/emboss/pkg-plist.EMNU
deleted file mode 100644
index fcb7fe6fe4a6..000000000000
--- a/biology/emboss/pkg-plist.EMNU
+++ /dev/null
@@ -1,2 +0,0 @@
-bin/emnu
-share/EMBOSS/acd/emnu.acd
diff --git a/biology/emboss/pkg-plist.MSE b/biology/emboss/pkg-plist.MSE
deleted file mode 100644
index eaa15866ab0a..000000000000
--- a/biology/emboss/pkg-plist.MSE
+++ /dev/null
@@ -1,6 +0,0 @@
-bin/mse
-lib/libckit.a
-lib/libckit.la
-lib/libckit.so
-lib/libckit.so.1
-share/EMBOSS/acd/mse.acd
diff --git a/biology/emboss/pkg-plist.PHYLIP b/biology/emboss/pkg-plist.PHYLIP
deleted file mode 100644
index a654ca4542ca..000000000000
--- a/biology/emboss/pkg-plist.PHYLIP
+++ /dev/null
@@ -1,48 +0,0 @@
-bin/eclique
-bin/econsense
-bin/econtml
-bin/econtrast
-bin/ednacomp
-bin/ednadist
-bin/ednainvar
-bin/ednaml
-bin/ednamlk
-bin/ednapars
-bin/ednapenny
-bin/edollop
-bin/edolpenny
-bin/efactor
-bin/efitch
-bin/egendist
-bin/ekitsch
-bin/emix
-bin/eneighbor
-bin/epenny
-bin/eprotdist
-bin/eprotpars
-bin/erestml
-bin/eseqboot
-share/EMBOSS/acd/eclique.acd
-share/EMBOSS/acd/econsense.acd
-share/EMBOSS/acd/econtml.acd
-share/EMBOSS/acd/econtrast.acd
-share/EMBOSS/acd/ednacomp.acd
-share/EMBOSS/acd/ednadist.acd
-share/EMBOSS/acd/ednainvar.acd
-share/EMBOSS/acd/ednaml.acd
-share/EMBOSS/acd/ednamlk.acd
-share/EMBOSS/acd/ednapars.acd
-share/EMBOSS/acd/ednapenny.acd
-share/EMBOSS/acd/edollop.acd
-share/EMBOSS/acd/edolpenny.acd
-share/EMBOSS/acd/efactor.acd
-share/EMBOSS/acd/efitch.acd
-share/EMBOSS/acd/egendist.acd
-share/EMBOSS/acd/ekitsch.acd
-share/EMBOSS/acd/emix.acd
-share/EMBOSS/acd/eneighbor.acd
-share/EMBOSS/acd/epenny.acd
-share/EMBOSS/acd/eprotdist.acd
-share/EMBOSS/acd/eprotpars.acd
-share/EMBOSS/acd/erestml.acd
-share/EMBOSS/acd/eseqboot.acd
diff --git a/biology/emboss/pkg-plist.TOPO b/biology/emboss/pkg-plist.TOPO
deleted file mode 100644
index 3be9738c819f..000000000000
--- a/biology/emboss/pkg-plist.TOPO
+++ /dev/null
@@ -1,2 +0,0 @@
-bin/topo
-share/EMBOSS/acd/topo.acd