- Update port to version 2.0.1

- Add two new EMBASSY applications, MEME and HMMER.

5 files changed, 110 insertions, 24 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 8d98b41cff66..52c50aea85e5 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.13.3
+PORTVERSION=	2.0.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
@@ -22,6 +22,7 @@ LIB_DEPENDS=	gd.2:${PORTSDIR}/graphics/gd
 
 USE_GMAKE=	yes
 USE_LIBTOOL=	yes
+INSTALLS_SHLIB=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
 PKGMESSAGE=	${WRKDIR}/pkg-message
@@ -38,13 +39,15 @@ SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
 WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
 EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
 EMNU_VERSION=	1.0.4
+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 MSE PHYLIP TOPO
+.for app in EMNU HMMER MEME MSE PHYLIP TOPO
 SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
 .if defined(WITH_${app})
 APPLIST+=	${app}
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 23a0d3c5749b..166c130b0274 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,5 +1,7 @@
-MD5 (emboss/EMBOSS-1.13.3.tar.gz) = ef3ebd34154abf04293f58bd9974267b
-MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
-MD5 (emboss/MSE-0.0.4.tar.gz) = d671afc3a3cc211f038f7752fb09c8f6
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 3539ae2d0753a6e95e60d59d0177c305
-MD5 (emboss/TOPO-0.1.tar.gz) = 8666694007cf866f5cdfe2aba7c01e3b
+MD5 (emboss/EMBOSS-2.0.1.tar.gz) = 7546441cc78be9054c4cdd5e24b97048
+MD5 (emboss/EMNU-1.0.4.tar.gz) = f24a5dcfe2cd7a4423f8dc8ed1946920
+MD5 (emboss/HMMER-2.1.1.tar.gz) = 01686894a1d5ca4b93555648e4e192bd
+MD5 (emboss/MEME-2.3.1.tar.gz) = 941921287a49a691d2a78b8726b5ac88
+MD5 (emboss/MSE-0.0.4.tar.gz) = 20661dce0e542b25d17bff86858f6cb2
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 55c91edc768003f83342f4c8e5b345e4
+MD5 (emboss/TOPO-0.1.tar.gz) = 416f5211bd9a7caee009c743e5a1a268
diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr
index 9ab6845287f8..2f1998bcc511 100644
--- a/biology/emboss/pkg-descr
+++ b/biology/emboss/pkg-descr
@@ -13,11 +13,11 @@ 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 currently available
-EMBASSY applications - EMNU, 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.
+EMBASSY applications.  During an interactive install the user will be asked
+to choose which of these will be installed (default: all).  Note that the
+EMBASSY versions of PHYLIP and HMMER should not clash with the standalone
+versions (also in ports/biology) due to the fact that their binaries have been
+renamed.
 
 WWW: http://www.emboss.org/
 
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index a559dc57ee5e..dc31f5f5c511 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -1,5 +1,35 @@
 %%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
@@ -72,6 +102,7 @@ bin/codcmp
 bin/coderet
 bin/compseq
 bin/cons
+bin/contacts
 bin/cpgplot
 bin/cpgreport
 bin/cusp
@@ -113,6 +144,7 @@ bin/getorf
 bin/helixturnhelix
 bin/hmoment
 bin/iep
+bin/infoalign
 bin/infoseq
 bin/isochore
 bin/lindna
@@ -171,6 +203,7 @@ bin/seealso
 bin/seqmatchall
 bin/seqret
 bin/seqretall
+bin/seqretallfeat
 bin/seqretset
 bin/seqretsplit
 bin/showalign
@@ -180,11 +213,13 @@ bin/showorf
 bin/showseq
 bin/shuffleseq
 bin/sigcleave
+bin/siggen
 bin/silent
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
+bin/swissparse
 bin/syco
 bin/textsearch
 bin/tfextract
@@ -216,7 +251,6 @@ share/EMBOSS/acd/abiview.acd
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
-share/EMBOSS/acd/ajtest2.acd
 share/EMBOSS/acd/antigenic.acd
 share/EMBOSS/acd/backtranseq.acd
 share/EMBOSS/acd/banana.acd
@@ -227,7 +261,6 @@ share/EMBOSS/acd/charge.acd
 share/EMBOSS/acd/checktrans.acd
 share/EMBOSS/acd/chips.acd
 share/EMBOSS/acd/cirdna.acd
-share/EMBOSS/acd/cluster.acd
 share/EMBOSS/acd/codcmp.acd
 share/EMBOSS/acd/coderet.acd
 share/EMBOSS/acd/codes.english
@@ -245,6 +278,7 @@ share/EMBOSS/acd/dbiblast.acd
 share/EMBOSS/acd/dbifasta.acd
 share/EMBOSS/acd/dbiflat.acd
 share/EMBOSS/acd/dbigcg.acd
+share/EMBOSS/acd/degapseq.acd
 share/EMBOSS/acd/demofeatures.acd
 share/EMBOSS/acd/demolist.acd
 share/EMBOSS/acd/demosequence.acd
@@ -253,6 +287,7 @@ share/EMBOSS/acd/demotable.acd
 share/EMBOSS/acd/descseq.acd
 share/EMBOSS/acd/diffseq.acd
 share/EMBOSS/acd/digest.acd
+share/EMBOSS/acd/distmat.acd
 share/EMBOSS/acd/domainer.acd
 share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dotpath.acd
@@ -281,6 +316,7 @@ share/EMBOSS/acd/helixturnhelix.acd
 share/EMBOSS/acd/histogramtest.acd
 share/EMBOSS/acd/hmoment.acd
 share/EMBOSS/acd/iep.acd
+share/EMBOSS/acd/infoalign.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
 share/EMBOSS/acd/lindna.acd
@@ -315,7 +351,6 @@ share/EMBOSS/acd/pepwindow.acd
 share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/plotcon.acd
 share/EMBOSS/acd/plotorf.acd
-share/EMBOSS/acd/plplottest.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
@@ -327,8 +362,8 @@ share/EMBOSS/acd/profit.acd
 share/EMBOSS/acd/prophecy.acd
 share/EMBOSS/acd/prophet.acd
 share/EMBOSS/acd/prosextract.acd
-share/EMBOSS/acd/proteinmotifsearch.acd
 share/EMBOSS/acd/pscan.acd
+share/EMBOSS/acd/psiblasts.acd
 share/EMBOSS/acd/rebaseextract.acd
 share/EMBOSS/acd/recoder.acd
 share/EMBOSS/acd/redata.acd
@@ -336,6 +371,7 @@ share/EMBOSS/acd/remap.acd
 share/EMBOSS/acd/restover.acd
 share/EMBOSS/acd/restrict.acd
 share/EMBOSS/acd/revseq.acd
+share/EMBOSS/acd/scopalign.acd
 share/EMBOSS/acd/scope.acd
 share/EMBOSS/acd/seealso.acd
 share/EMBOSS/acd/seqinfo.acd
@@ -343,11 +379,9 @@ share/EMBOSS/acd/seqmatchall.acd
 share/EMBOSS/acd/seqret.acd
 share/EMBOSS/acd/seqretall.acd
 share/EMBOSS/acd/seqretallfeat.acd
-share/EMBOSS/acd/seqretfeat.acd
 share/EMBOSS/acd/seqretset.acd
 share/EMBOSS/acd/seqretsplit.acd
 share/EMBOSS/acd/seqrettype.acd
-share/EMBOSS/acd/seqtofeat.acd
 share/EMBOSS/acd/showalign.acd
 share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/showfeat.acd
@@ -355,10 +389,10 @@ share/EMBOSS/acd/showorf.acd
 share/EMBOSS/acd/showseq.acd
 share/EMBOSS/acd/shuffleseq.acd
 share/EMBOSS/acd/sigcleave.acd
+share/EMBOSS/acd/siggen.acd
+share/EMBOSS/acd/sigscan.acd
 share/EMBOSS/acd/silent.acd
-share/EMBOSS/acd/simplesw.acd
 share/EMBOSS/acd/splitter.acd
-share/EMBOSS/acd/stamps.acd
 share/EMBOSS/acd/stretcher.acd
 share/EMBOSS/acd/stssearch.acd
 share/EMBOSS/acd/supermatcher.acd
@@ -630,7 +664,11 @@ share/EMBOSS/data/Edna.melt
 share/EMBOSS/data/Eembl.ior
 share/EMBOSS/data/Eenergy.dat
 share/EMBOSS/data/Efeatures.embl
+share/EMBOSS/data/Efeatures.emboss
 share/EMBOSS/data/Efeatures.gff
+share/EMBOSS/data/Efeatures.pir
+share/EMBOSS/data/Efeatures.protein
+share/EMBOSS/data/Efeatures.swiss
 share/EMBOSS/data/Efreqs.dat
 share/EMBOSS/data/Ehth.dat
 share/EMBOSS/data/Ehth87.dat
@@ -645,7 +683,11 @@ share/EMBOSS/data/Erna.melt
 share/EMBOSS/data/Esig.euk
 share/EMBOSS/data/Esig.pro
 share/EMBOSS/data/Etags.embl
+share/EMBOSS/data/Etags.emboss
 share/EMBOSS/data/Etags.gff
+share/EMBOSS/data/Etags.pir
+share/EMBOSS/data/Etags.protein
+share/EMBOSS/data/Etags.swiss
 share/EMBOSS/data/Ewhite-wimley.dat
 share/EMBOSS/data/PRINTS/dummyfile
 share/EMBOSS/data/PROSITE/dummyfile
@@ -680,6 +722,9 @@ share/EMBOSS/test/data/dna.phylip3
 share/EMBOSS/test/data/dna.staden
 share/EMBOSS/test/data/dna.strider
 share/EMBOSS/test/data/dna.text
+share/EMBOSS/test/data/feat.emft
+share/EMBOSS/test/data/feat.fasta
+share/EMBOSS/test/data/feat.pir
 share/EMBOSS/test/data/paamir.pep
 share/EMBOSS/test/data/prot.acedb
 share/EMBOSS/test/data/prot.codata
@@ -705,10 +750,16 @@ share/EMBOSS/test/embl/est.dat
 share/EMBOSS/test/embl/fun.dat
 share/EMBOSS/test/embl/hum1.dat
 share/EMBOSS/test/embl/inv.dat
+share/EMBOSS/test/embl/pln.dat
 share/EMBOSS/test/embl/pro.dat
 share/EMBOSS/test/embl/rod.dat
+share/EMBOSS/test/embl/sts.dat
 share/EMBOSS/test/embl/vrl.dat
 share/EMBOSS/test/embl/vrt.dat
+share/EMBOSS/test/pir/acnum.hit
+share/EMBOSS/test/pir/acnum.trg
+share/EMBOSS/test/pir/division.lkp
+share/EMBOSS/test/pir/entrynam.idx
 share/EMBOSS/test/pir/pir1.header
 share/EMBOSS/test/pir/pir1.names
 share/EMBOSS/test/pir/pir1.numbers
@@ -789,6 +840,7 @@ share/doc/EMBOSS/programs/html/coderet.html
 share/doc/EMBOSS/programs/html/compseq.html
 share/doc/EMBOSS/programs/html/cons.html
 share/doc/EMBOSS/programs/html/consense.html
+share/doc/EMBOSS/programs/html/contacts.html
 share/doc/EMBOSS/programs/html/contml.html
 share/doc/EMBOSS/programs/html/contrast.html
 share/doc/EMBOSS/programs/html/cpgplot.html
@@ -844,9 +896,9 @@ share/doc/EMBOSS/programs/html/einverted.html
 share/doc/EMBOSS/programs/html/ekitsch.html
 share/doc/EMBOSS/programs/html/emboss_icon.gif
 share/doc/EMBOSS/programs/html/embossdata.html
+share/doc/EMBOSS/programs/html/embossversion.html
 share/doc/EMBOSS/programs/html/emix.html
 share/doc/EMBOSS/programs/html/emma.html
-share/doc/EMBOSS/programs/html/emnu.html
 share/doc/EMBOSS/programs/html/emowse.html
 share/doc/EMBOSS/programs/html/eneighbor.html
 share/doc/EMBOSS/programs/html/entret.html
@@ -878,6 +930,7 @@ share/doc/EMBOSS/programs/html/helixturnhelix.html
 share/doc/EMBOSS/programs/html/hmoment.html
 share/doc/EMBOSS/programs/html/iep.html
 share/doc/EMBOSS/programs/html/index.html
+share/doc/EMBOSS/programs/html/infoalign.html
 share/doc/EMBOSS/programs/html/information_group.html
 share/doc/EMBOSS/programs/html/infoseq.html
 share/doc/EMBOSS/programs/html/isochore.html
@@ -963,6 +1016,7 @@ share/doc/EMBOSS/programs/html/protein_composition_group.html
 share/doc/EMBOSS/programs/html/protein_motifs_group.html
 share/doc/EMBOSS/programs/html/protein_mutation_group.html
 share/doc/EMBOSS/programs/html/protein_profiles_group.html
+share/doc/EMBOSS/programs/html/protein_structure_group.html
 share/doc/EMBOSS/programs/html/pscan.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
 share/doc/EMBOSS/programs/html/recode.html
@@ -973,26 +1027,33 @@ share/doc/EMBOSS/programs/html/restml.html
 share/doc/EMBOSS/programs/html/restover.html
 share/doc/EMBOSS/programs/html/restrict.html
 share/doc/EMBOSS/programs/html/revseq.html
+share/doc/EMBOSS/programs/html/scopalign.html
 share/doc/EMBOSS/programs/html/scope.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqboot.html
 share/doc/EMBOSS/programs/html/seqmatchall.html
 share/doc/EMBOSS/programs/html/seqret.html
 share/doc/EMBOSS/programs/html/seqretall.html
+share/doc/EMBOSS/programs/html/seqretallfeat.html
 share/doc/EMBOSS/programs/html/seqretfeat.html
 share/doc/EMBOSS/programs/html/seqretset.html
 share/doc/EMBOSS/programs/html/seqretsplit.html
+share/doc/EMBOSS/programs/html/showalign.html
 share/doc/EMBOSS/programs/html/showdb.html
 share/doc/EMBOSS/programs/html/showfeat.html
 share/doc/EMBOSS/programs/html/showorf.html
 share/doc/EMBOSS/programs/html/showseq.html
 share/doc/EMBOSS/programs/html/shuffleseq.html
 share/doc/EMBOSS/programs/html/sigcleave.html
+share/doc/EMBOSS/programs/html/siggen.html
+share/doc/EMBOSS/programs/html/sigscan.html
 share/doc/EMBOSS/programs/html/silent.html
 share/doc/EMBOSS/programs/html/splitter.html
+share/doc/EMBOSS/programs/html/stamps.html
 share/doc/EMBOSS/programs/html/stretcher.html
 share/doc/EMBOSS/programs/html/stssearch.html
 share/doc/EMBOSS/programs/html/supermatcher.html
+share/doc/EMBOSS/programs/html/swissparse.html
 share/doc/EMBOSS/programs/html/syco.html
 share/doc/EMBOSS/programs/html/syco0.gif
 share/doc/EMBOSS/programs/html/syco1.gif
@@ -1036,6 +1097,7 @@ share/doc/EMBOSS/programs/text/complex.txt
 share/doc/EMBOSS/programs/text/compseq.txt
 share/doc/EMBOSS/programs/text/cons.txt
 share/doc/EMBOSS/programs/text/consense.txt
+share/doc/EMBOSS/programs/text/contacts.txt
 share/doc/EMBOSS/programs/text/contml.txt
 share/doc/EMBOSS/programs/text/contrast.txt
 share/doc/EMBOSS/programs/text/cpgplot.txt
@@ -1085,9 +1147,9 @@ share/doc/EMBOSS/programs/text/egendist.txt
 share/doc/EMBOSS/programs/text/einverted.txt
 share/doc/EMBOSS/programs/text/ekitsch.txt
 share/doc/EMBOSS/programs/text/embossdata.txt
+share/doc/EMBOSS/programs/text/embossversion.txt
 share/doc/EMBOSS/programs/text/emix.txt
 share/doc/EMBOSS/programs/text/emma.txt
-share/doc/EMBOSS/programs/text/emnu.txt
 share/doc/EMBOSS/programs/text/emowse.txt
 share/doc/EMBOSS/programs/text/eneighbor.txt
 share/doc/EMBOSS/programs/text/entret.txt
@@ -1114,6 +1176,7 @@ share/doc/EMBOSS/programs/text/getorf.txt
 share/doc/EMBOSS/programs/text/helixturnhelix.txt
 share/doc/EMBOSS/programs/text/hmoment.txt
 share/doc/EMBOSS/programs/text/iep.txt
+share/doc/EMBOSS/programs/text/infoalign.txt
 share/doc/EMBOSS/programs/text/infoseq.txt
 share/doc/EMBOSS/programs/text/isochore.txt
 share/doc/EMBOSS/programs/text/kitsch.txt
@@ -1174,26 +1237,33 @@ share/doc/EMBOSS/programs/text/restml.txt
 share/doc/EMBOSS/programs/text/restover.txt
 share/doc/EMBOSS/programs/text/restrict.txt
 share/doc/EMBOSS/programs/text/revseq.txt
+share/doc/EMBOSS/programs/text/scopalign.txt
 share/doc/EMBOSS/programs/text/scope.txt
 share/doc/EMBOSS/programs/text/seealso.txt
 share/doc/EMBOSS/programs/text/seqboot.txt
 share/doc/EMBOSS/programs/text/seqmatchall.txt
 share/doc/EMBOSS/programs/text/seqret.txt
 share/doc/EMBOSS/programs/text/seqretall.txt
+share/doc/EMBOSS/programs/text/seqretallfeat.txt
 share/doc/EMBOSS/programs/text/seqretfeat.txt
 share/doc/EMBOSS/programs/text/seqretset.txt
 share/doc/EMBOSS/programs/text/seqretsplit.txt
+share/doc/EMBOSS/programs/text/showalign.txt
 share/doc/EMBOSS/programs/text/showdb.txt
 share/doc/EMBOSS/programs/text/showfeat.txt
 share/doc/EMBOSS/programs/text/showorf.txt
 share/doc/EMBOSS/programs/text/showseq.txt
 share/doc/EMBOSS/programs/text/shuffleseq.txt
 share/doc/EMBOSS/programs/text/sigcleave.txt
+share/doc/EMBOSS/programs/text/siggen.txt
+share/doc/EMBOSS/programs/text/sigscan.txt
 share/doc/EMBOSS/programs/text/silent.txt
 share/doc/EMBOSS/programs/text/splitter.txt
+share/doc/EMBOSS/programs/text/stamps.txt
 share/doc/EMBOSS/programs/text/stretcher.txt
 share/doc/EMBOSS/programs/text/stssearch.txt
 share/doc/EMBOSS/programs/text/supermatcher.txt
+share/doc/EMBOSS/programs/text/swissparse.txt
 share/doc/EMBOSS/programs/text/syco.txt
 share/doc/EMBOSS/programs/text/textsearch.txt
 share/doc/EMBOSS/programs/text/tfextract.txt
@@ -1211,7 +1281,10 @@ share/doc/EMBOSS/programs/text/wordmatch.txt
 share/doc/EMBOSS/programs/text/wossname.txt
 share/doc/EMBOSS/tutorials/biblio.bib
 share/doc/EMBOSS/tutorials/dottup.ps.gz
+share/doc/EMBOSS/tutorials/emboss-gcg.ppt
+share/doc/EMBOSS/tutorials/emboss-interfaces.ppt
 share/doc/EMBOSS/tutorials/emboss-talk.ppt
+share/doc/EMBOSS/tutorials/emboss_tutorial.ps.gz
 share/doc/EMBOSS/tutorials/emboss_tutorial.tex
 share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
 share/doc/EMBOSS/tutorials/pepinfo2.ps.gz
diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss
index b5ad7348def5..b14bb8e85d8b 100644
--- a/biology/emboss/scripts/configure.emboss
+++ b/biology/emboss/scripts/configure.emboss
@@ -5,14 +5,16 @@ if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
 fi
 
 if [ "${BATCH}" ]; then
-  set \"EMNU\" \"MSE\" \"PHYLIP\" \"TOPO\"
+  set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\"
 else
   /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
   --checklist "\n\
 These third party applications have been adapted to
 function as part of EMBOSS.\n
-Please select EMBASSY applications to install:" -1 -1 4 \
+Please select EMBASSY applications to install:" -1 -1 6 \
 EMNU	"v${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 \
@@ -46,6 +48,12 @@ while [ "$1" ]; do
     \"EMNU\")
       echo "WITH_EMNU=	yes"
     ;;
+    \"HMMER\")
+      echo "WITH_HMMER=	yes"
+    ;;
+    \"MEME\")
+      echo "WITH_MEME=	yes"
+    ;;
     \"MSE\")
       echo "WITH_MSE=	yes"
     ;;