- Update to 2.9.0

- Pass maintainership to submitter

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

9 files changed, 1632 insertions, 1812 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>
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index bcc2cea1e109..5c53ea980ba9 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,7 +1,2 @@
-MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad
-MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66
-MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
-MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
-MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
-MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a
+MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472
+SIZE (EMBOSS-2.9.0.tar.gz) = 14479274
diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa
deleted file mode 100644
index 60853ff96c11..000000000000
--- a/biology/emboss/files/patch-aa
+++ /dev/null
@@ -1,26 +0,0 @@
-Add ${PREFIX}/etc as an acceptable location for emboss.default.  (I'm still
-waiting for this to be incorporated into an official release of EMBOSS.)
-
-The port installs ${PREFIX}/etc/emboss.default.sample
-
--- Johann <wjv@FreeBSD.org>
-
-
---- ajax/ajnam.c.orig	Thu Aug 17 20:31:30 2000
-+++ ajax/ajnam.c	Mon Aug 28 15:12:09 2000
-@@ -984,6 +984,15 @@
- 	prefixRootFile = fopen (ajStrStr(namRootStr), "r");
-     }
- 
-+    /* look for $(PREFIX)_ROOT/../emboss.default */
-+
-+    if (!prefixRootFile)
-+    {
-+      ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
-+		   namInstallRoot, prefix);
-+      prefixRootFile = fopen (ajStrStr(namRootStr), "r");
-+    }
-+
-     if (namFileOrig)
- 	(void) ajStrAppC (&namFileOrig, ", ");
-     (void) ajStrApp (&namFileOrig, namRootStr);
diff --git a/biology/emboss/files/patch-ajax::ajjava.c b/biology/emboss/files/patch-ajax::ajjava.c
deleted file mode 100644
index 76189b95c03b..000000000000
--- a/biology/emboss/files/patch-ajax::ajjava.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- ajax/ajjava.c.orig	Thu May  2 22:06:08 2002
-+++ ajax/ajjava.c	Sun May 26 09:14:20 2002
-@@ -75,7 +75,7 @@
- #endif
- 
- #ifndef __ppc__
--#include <crypt.h>
-+#include <unistd.h>
- #endif
- 
- 
diff --git a/biology/emboss/files/patch-configure b/biology/emboss/files/patch-configure
deleted file mode 100644
index da46a3c60faa..000000000000
--- a/biology/emboss/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	Mon Jan 22 23:28:17 2001
-+++ configure	Thu Jan 25 19:07:33 2001
-@@ -1473,7 +1473,7 @@
- 
- 
- 
--AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
-+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
- 
- #AC_PROG_CXX
- for ac_prog in mawk gawk nawk awk
diff --git a/biology/emboss/files/patch-emboss-emboss.default.template b/biology/emboss/files/patch-emboss-emboss.default.template
deleted file mode 100644
index 3bbe6641a0d1..000000000000
--- a/biology/emboss/files/patch-emboss-emboss.default.template
+++ /dev/null
@@ -1,38 +0,0 @@
---- emboss/emboss.default.template.orig	Thu May 24 19:36:39 2001
-+++ emboss/emboss.default.template	Wed May 30 10:23:48 2001
-@@ -1,9 +1,31 @@
--#SET emboss_tempdata name_of_emboss_test_database_directory
-+#####################################################
-+### 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
-+# The directory where EMBOSS expects to find run-time
-+# databases.  This is the compiled-in default - change
-+# only if you know what you're doing!
-+#
-+#SET emboss_data %%PREFIX%%/share/EMBOSS/data
- 
--#SET emboss_logfile /packages/emboss/emboss/log
-+# This is an alias which is internal to this
-+# configuration file and is set here merely as a
-+# convenience.  It points to the location where you
-+# have placed your local databases (this will differ
-+# from site to site).
-+#
-+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
-+
-+# Logfile.  If this is uncommented and set to a file
-+# that any user can append to, EMBOSS applications
-+# will automatically log usage information.
-+#
-+#SET emboss_logfile /var/log/emboss.log
-+
-+
-+###########################################
-+### Configuration options for databases ###
-+###########################################
- 
- # swissprot (Puffer fish entries)
- # =========
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
index 31845abb7690..1c36c80c0b39 100644
--- a/biology/emboss/pkg-message
+++ b/biology/emboss/pkg-message
@@ -15,7 +15,8 @@ A .embossrc in a user's home directory overrides settings in the
 system-wide emboss.default.
 
 Online EMBOSS documentation is available at:
-	http://www.uk.embnet.org/Software/EMBOSS/general.html
+	http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
 	http://www.uk.embnet.org/Software/EMBOSS/Doc/
+  http://emboss.sourceforge.net/docs/
 
 --------------------------------------------------------------------------
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 7db872665c01..ce1ef92d70f0 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -1,94 +1,10 @@
-%%PLIST_EMNU%%bin/emnu
-%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
-%%PLIST_HMMER%%bin/ealistat
-%%PLIST_HMMER%%bin/ehmmalign
-%%PLIST_HMMER%%bin/ehmmbuild
-%%PLIST_HMMER%%bin/ehmmcalibrate
-%%PLIST_HMMER%%bin/ehmmconvert
-%%PLIST_HMMER%%bin/ehmmemit
-%%PLIST_HMMER%%bin/ehmmfetch
-%%PLIST_HMMER%%bin/ehmmindex
-%%PLIST_HMMER%%bin/ehmmpfam
-%%PLIST_HMMER%%bin/ehmmsearch
-%%PLIST_HMMER%%lib/libhmmer.a
-%%PLIST_HMMER%%lib/libhmmer.la
-%%PLIST_HMMER%%lib/libhmmer.so
-%%PLIST_HMMER%%lib/libhmmer.so.2
-%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
-%%PLIST_MEME%%bin/meme
-%%PLIST_MEME%%lib/libmeme.a
-%%PLIST_MEME%%lib/libmeme.la
-%%PLIST_MEME%%lib/libmeme.so
-%%PLIST_MEME%%lib/libmeme.so.2
-%%PLIST_MEME%%share/EMBOSS/acd/meme.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/aaindexextract
 bin/abiview
 bin/acdc
-bin/alignwrap
+bin/acdpretty
+bin/acdtable
+bin/acdtrace
+bin/acdvalid
 bin/antigenic
 bin/backtranseq
 bin/banana
@@ -104,7 +20,6 @@ bin/codcmp
 bin/coderet
 bin/compseq
 bin/cons
-bin/contacts
 bin/cpgplot
 bin/cpgreport
 bin/cusp
@@ -117,11 +32,9 @@ bin/dbiflat
 bin/dbigcg
 bin/degapseq
 bin/descseq
-bin/dichet
 bin/diffseq
 bin/digest
 bin/distmat
-bin/domainer
 bin/dotmatcher
 bin/dotpath
 bin/dottup
@@ -132,6 +45,7 @@ bin/embossversion
 bin/emma
 bin/emowse
 bin/entret
+bin/epestfind
 bin/eprimer3
 bin/equicktandem
 bin/est2genome
@@ -151,7 +65,6 @@ bin/hmoment
 bin/iep
 bin/infoalign
 bin/infoseq
-bin/interface
 bin/isochore
 bin/jembossctl
 bin/lindna
@@ -163,14 +76,14 @@ bin/matcher
 bin/megamerger
 bin/merger
 bin/msbar
+bin/mwcontam
 bin/mwfilter
 bin/needle
 bin/newcpgreport
 bin/newcpgseek
 bin/newseq
-bin/noreturn
 bin/notseq
-bin/nrscope
+bin/noreturn
 bin/nthseq
 bin/octanol
 bin/oddcomp
@@ -178,7 +91,6 @@ bin/palindrome
 bin/pasteseq
 bin/patmatdb
 bin/patmatmotifs
-bin/pdbtosp
 bin/pepcoil
 bin/pepinfo
 bin/pepnet
@@ -199,7 +111,7 @@ bin/prophecy
 bin/prophet
 bin/prosextract
 bin/pscan
-bin/psiblasts
+bin/psiphi
 bin/rebaseextract
 bin/recoder
 bin/redata
@@ -207,16 +119,10 @@ bin/remap
 bin/restover
 bin/restrict
 bin/revseq
-bin/runJemboss.csh
-bin/scopalign
-bin/scope
-bin/scopparse
 bin/seealso
 bin/seqmatchall
-bin/seqnr
 bin/seqret
 bin/seqretsplit
-bin/seqsort
 bin/showalign
 bin/showdb
 bin/showfeat
@@ -224,15 +130,16 @@ bin/showorf
 bin/showseq
 bin/shuffleseq
 bin/sigcleave
-bin/siggen
-bin/sigscan
 bin/silent
+bin/sirna
+bin/sixpack
+bin/skipseq
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
-bin/swissparse
 bin/syco
+bin/tcode
 bin/textsearch
 bin/tfextract
 bin/tfm
@@ -242,6 +149,7 @@ bin/tranalign
 bin/transeq
 bin/trimest
 bin/trimseq
+bin/twofeat
 bin/union
 bin/vectorstrip
 bin/water
@@ -251,1441 +159,1598 @@ bin/wordcount
 bin/wordmatch
 bin/wossname
 bin/yank
+bin/runJemboss.csh
 etc/emboss.default.sample
-lib/libajax.a
-lib/libajax.la
-lib/libajax.so
+include/drivers.h
+include/pdf.h
+include/plcore.h
+include/plevent.h
+include/plplotP.h
+include/plxwd.h
+include/metadefs.h
+include/plConfig.h
+include/pldebug.h
+include/plplot.h
+include/plstrm.h
+include/plDevs.h
+include/ajax.h
+include/ajarch.h
+include/ajdefine.h
+include/ajacd.h
+include/ajalign.h
+include/ajarr.h
+include/ajassert.h
+include/ajbase.h
+include/ajcall.h
+include/ajcod.h
+include/ajdan.h
+include/ajdmx.h
+include/ajdomain.h
+include/ajexcept.h
+include/ajfeat.h
+include/ajfeatdata.h
+include/ajfile.h
+include/ajfmt.h
+include/ajgraph.h
+include/ajgraphxml.h
+include/ajgraphstruct.h
+include/ajhist.h
+include/ajjava.h
+include/ajlist.h
+include/ajmath.h
+include/ajmatrices.h
+include/ajmem.h
+include/ajmess.h
+include/ajnam.h
+include/ajnexus.h
+include/ajpdb.h
+include/ajpdbio.h
+include/ajphylo.h
+include/ajrange.h
+include/ajreg.h
+include/ajreport.h
+include/ajseq.h
+include/ajseqabi.h
+include/ajseqdata.h
+include/ajseqdb.h
+include/ajseqread.h
+include/ajseqtype.h
+include/ajseqwrite.h
+include/ajsort.h
+include/ajstr.h
+include/ajsys.h
+include/ajtable.h
+include/ajtime.h
+include/ajtranslate.h
+include/ajtree.h
+include/ajutil.h
+include/ajvector.h
+include/pcre.h
+include/pcre_chartables.c
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+include/pcre_get.c
+include/pcre_printint.c
+include/pcre_internal.h
+include/pcreposix.h
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+include/embdata.h
+include/embdbi.h
+include/embdmx.h
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+include/embexit.h
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+include/embmat.h
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+include/embmol.h
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+include/embpat.h
+include/embprop.h
+include/embpdb.h
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+include/embsig.h
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+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/OutputSequenceAttributes.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
+%%DATADIR%%/jemboss/resources/jemboss.properties
+%%DATADIR%%/jemboss/resources/readme.html
+%%DATADIR%%/jemboss/resources/readmeAlign.html
+%%DATADIR%%/jemboss/resources/readmeDNADraw.html
+%%DATADIR%%/jemboss/resources/results.html
+%%DATADIR%%/jemboss/resources/version
+%%DATADIR%%/jemboss/resources/filemgr.html
+%%DATADIR%%/jemboss/resources/seqList.html
+%%DATADIR%%/jemboss/utils/install-jemboss-server.sh
+%%DATADIR%%/jemboss/utils/keys.sh
+%%DATADIR%%/jemboss/utils/makeJar.csh
+%%DATADIR%%/jemboss/utils/makeJNLP.sh
+%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
+%%DATADIR%%/jemboss/utils/template.html
+%%DATADIR%%/jemboss/utils/README
+%%DATADIR%%/jemboss/LICENSE
+%%DATADIR%%/jemboss/readme.html
+%%DATADIR%%/jemboss/runJemboss.sh
+%%DATADIR%%/jemboss/README
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%/acd
+@dirrm %%DATADIR%%/data/AAINDEX
+@dirrm %%DATADIR%%/data/CODONS
+@dirrm %%DATADIR%%/data/REBASE
+@dirrm %%DATADIR%%/data/PRINTS
+@dirrm %%DATADIR%%/data/PROSITE
+@dirrm %%DATADIR%%/data
+@dirrm %%DATADIR%%/test/data
+@dirrm %%DATADIR%%/test/embl
+@dirrm %%DATADIR%%/test/genbank
+@dirrm %%DATADIR%%/test/gb
+@dirrm %%DATADIR%%/test/pir
+@dirrm %%DATADIR%%/test/swiss
+@dirrm %%DATADIR%%/test/swnew
+@dirrm %%DATADIR%%/test/wormpep
+@dirrm %%DATADIR%%/test
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss
+@dirrm %%DATADIR%%/jemboss/api/org/emboss
+@dirrm %%DATADIR%%/jemboss/api/org
+@dirrm %%DATADIR%%/jemboss/api
+@dirrm %%DATADIR%%/jemboss/images
+@dirrm %%DATADIR%%/jemboss/lib/axis
+@dirrm %%DATADIR%%/jemboss/lib
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
+@dirrm %%DATADIR%%/jemboss/org/emboss
+@dirrm %%DATADIR%%/jemboss/org
+@dirrm %%DATADIR%%/jemboss/resources
+@dirrm %%DATADIR%%/jemboss/utils
+@dirrm %%DATADIR%%/jemboss
+@dirrm %%DATADIR%%
diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss
deleted file mode 100644
index b14bb8e85d8b..000000000000
--- a/biology/emboss/scripts/configure.emboss
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/bin/sh
-
-if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
-  exit
-fi
-
-if [ "${BATCH}" ]; then
-  set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\"
-else
-  /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
-  --checklist "\n\
-These third party applications have been adapted to
-function as part of EMBOSS.\n
-Please select EMBASSY applications to install:" -1 -1 6 \
-EMNU	"v${EMNU_VERSION} - Text-based menu" ON \
-HMMER	"v${HMMER_VERSION} - HMM alignment" ON \
-MEME	"v${MEME_VERSION} - Motif detection" ON \
-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
-    \"EMNU\")
-      echo "WITH_EMNU=	yes"
-    ;;
-    \"HMMER\")
-      echo "WITH_HMMER=	yes"
-    ;;
-    \"MEME\")
-      echo "WITH_MEME=	yes"
-    ;;
-    \"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