- Update port biology/emboss from 1.7.0 to 1.8.0

PR:		23130
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER

4 files changed, 124 insertions, 17 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index efe3acf09cb3..5db1e613d53b 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,14 +6,13 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.7.0
-PORTREVISION=	1
+PORTVERSION=	1.8.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/
-DISTFILES=	${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX}
+DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 DIST_SUBDIR=	${PORTNAME}
-EXTRACT_ONLY=	${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX}
+EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 
 MAINTAINER=	johann@egenetics.com
 
@@ -24,9 +23,7 @@ USE_GMAKE=	yes
 USE_LIBTOOL=	yes
 USE_XLIB=	yes
 PLIST=		${WRKDIR}/pkg-plist
-
-# Make doesn't know about :U
-PORTNAME_U=	EMBOSS
+PKGMESSAGE=	${WRKDIR}/pkg-message
 
 .if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
 .include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
@@ -39,7 +36,7 @@ SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
 		MKDIR="${MKDIR}" \
 		RM="${RM}"
 
-WRKSRC=		${WRKDIR}/${PORTNAME_U}-${PORTVERSION}
+WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
 EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
 PHYLIP_VERSION=	3.573c
 MSE_VERSION=	0.0.4
@@ -109,6 +106,8 @@ post-install:
 	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
 	  ${PREFIX}/etc/emboss.default.sample
 .if !defined(BATCH)
+	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
+	  pkg-message > ${PKGMESSAGE}
 	@ ${CAT} ${PKGMESSAGE}
 .endif
 
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 72b54429db4b..6ca3bb9a5140 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,4 +1,4 @@
-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
+MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4cbc80557dbbe41fbedb477e00e47aba
+MD5 (emboss/MSE-0.0.4.tar.gz) = 800216297fa6c3de76f6d1d7ea194a22
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = bd2ded015838da4236c3d4ac25ae8ede
+MD5 (emboss/TOPO-0.1.tar.gz) = 42f4f6e57e4c99b4684b0a4810f2c0a0
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
index a34183b481ce..22386f8457b6 100644
--- a/biology/emboss/pkg-message
+++ b/biology/emboss/pkg-message
@@ -3,13 +3,12 @@
 The EMBOSS suite has been successfully installed.
 
 In order to use the EMBOSS programs, you will need to set some environment
-variables in your shell startup file.  If EMBOSS was installed to the
-default prefix, then:
+variables in your shell startup file.
 
-- set PLPLOT_LIB to:     "/usr/local/share/EMBOSS"
-- set EMBOSS_ACDROOT to: "/usr/local/share/EMBOSS/acd"
+- set PLPLOT_LIB to:     "%%PREFIX%%/share/EMBOSS"
+- set EMBOSS_ACDROOT to: "%%PREFIX%%/share/EMBOSS/acd"
 
-NB:  A sample configuration file has been installed to /usr/local/etc as
+NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
 emboss.default.sample.  This must be renamed to emboss.default and edited
 to suit your site and its requirements.
 
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 4eb442cef213..0c277d0ee003 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -8,6 +8,7 @@ bin/checktrans
 bin/chips
 bin/cirdna
 bin/codcmp
+bin/coderet
 bin/complex
 bin/compseq
 bin/cons
@@ -151,10 +152,12 @@ 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
 share/EMBOSS/acd/complex.acd
 share/EMBOSS/acd/compseq.acd
 share/EMBOSS/acd/cons.acd
+share/EMBOSS/acd/corbatest.acd
 share/EMBOSS/acd/cpgplot.acd
 share/EMBOSS/acd/cpgreport.acd
 share/EMBOSS/acd/cusp.acd
@@ -248,6 +251,7 @@ share/EMBOSS/acd/redata.acd
 share/EMBOSS/acd/remap.acd
 share/EMBOSS/acd/restrict.acd
 share/EMBOSS/acd/revseq.acd
+share/EMBOSS/acd/scope.acd
 share/EMBOSS/acd/seealso.acd
 share/EMBOSS/acd/seqinfo.acd
 share/EMBOSS/acd/seqmatchall.acd
@@ -532,16 +536,20 @@ share/EMBOSS/data/Eantigenic.dat
 share/EMBOSS/data/Ebases.iub
 share/EMBOSS/data/Edayhoff.freq
 share/EMBOSS/data/Edna.melt
+share/EMBOSS/data/Eembl.ior
 share/EMBOSS/data/Eenergy.dat
 share/EMBOSS/data/Efeatures.embl
 share/EMBOSS/data/Efeatures.gff
 share/EMBOSS/data/Efreqs.dat
 share/EMBOSS/data/Ehth.dat
 share/EMBOSS/data/Ehth87.dat
+share/EMBOSS/data/Ememe.dat
 share/EMBOSS/data/Enakai.dat
 share/EMBOSS/data/Epepcoil.dat
 share/EMBOSS/data/Epk.dat
 share/EMBOSS/data/Epprofile
+share/EMBOSS/data/Eprior1.plib
+share/EMBOSS/data/Eprior30.plib
 share/EMBOSS/data/Erna.melt
 share/EMBOSS/data/Esig.euk
 share/EMBOSS/data/Esig.pro
@@ -666,12 +674,17 @@ share/doc/EMBOSS/programs/html/chaos0.gif
 share/doc/EMBOSS/programs/html/checktrans.html
 share/doc/EMBOSS/programs/html/chips.html
 share/doc/EMBOSS/programs/html/cirdna.html
+share/doc/EMBOSS/programs/html/clique.html
 share/doc/EMBOSS/programs/html/codcmp.html
+share/doc/EMBOSS/programs/html/coderet.html
 share/doc/EMBOSS/programs/html/coding_regions_group.html
 share/doc/EMBOSS/programs/html/comparison_group.html
 share/doc/EMBOSS/programs/html/complex.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/contml.html
+share/doc/EMBOSS/programs/html/contrast.html
 share/doc/EMBOSS/programs/html/cpg_islands_group.html
 share/doc/EMBOSS/programs/html/cpgplot.html
 share/doc/EMBOSS/programs/html/cpgplot0.gif
@@ -693,31 +706,67 @@ share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html
 share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html
 share/doc/EMBOSS/programs/html/dna_sequence_features_group.html
 share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html
+share/doc/EMBOSS/programs/html/dnacomp.html
+share/doc/EMBOSS/programs/html/dnadist.html
+share/doc/EMBOSS/programs/html/dnainvar.html
+share/doc/EMBOSS/programs/html/dnaml.html
+share/doc/EMBOSS/programs/html/dnamlk.html
+share/doc/EMBOSS/programs/html/dnapars.html
+share/doc/EMBOSS/programs/html/dnapenny.html
+share/doc/EMBOSS/programs/html/dollop.html
+share/doc/EMBOSS/programs/html/dolpenny.html
 share/doc/EMBOSS/programs/html/dotmatcher.html
 share/doc/EMBOSS/programs/html/dotmatcher0.gif
 share/doc/EMBOSS/programs/html/dotpath.html
 share/doc/EMBOSS/programs/html/dottup.html
 share/doc/EMBOSS/programs/html/dottup0.gif
 share/doc/EMBOSS/programs/html/dreg.html
+share/doc/EMBOSS/programs/html/eclique.html
+share/doc/EMBOSS/programs/html/econsense.html
+share/doc/EMBOSS/programs/html/econtml.html
+share/doc/EMBOSS/programs/html/econtrast.html
+share/doc/EMBOSS/programs/html/ednacomp.html
+share/doc/EMBOSS/programs/html/ednadist.html
+share/doc/EMBOSS/programs/html/ednainvar.html
+share/doc/EMBOSS/programs/html/ednaml.html
+share/doc/EMBOSS/programs/html/ednamlk.html
+share/doc/EMBOSS/programs/html/ednapars.html
+share/doc/EMBOSS/programs/html/ednapenny.html
+share/doc/EMBOSS/programs/html/edollop.html
+share/doc/EMBOSS/programs/html/edolpenny.html
+share/doc/EMBOSS/programs/html/efactor.html
+share/doc/EMBOSS/programs/html/efitch.html
+share/doc/EMBOSS/programs/html/egendist.html
 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/emix.html
 share/doc/EMBOSS/programs/html/emma.html
 share/doc/EMBOSS/programs/html/emowse.html
+share/doc/EMBOSS/programs/html/eneighbor.html
 share/doc/EMBOSS/programs/html/entret.html
 share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
+share/doc/EMBOSS/programs/html/epenny.html
+share/doc/EMBOSS/programs/html/eprotdist.html
+share/doc/EMBOSS/programs/html/eprotpars.html
 share/doc/EMBOSS/programs/html/equicktandem.html
+share/doc/EMBOSS/programs/html/erestml.html
+share/doc/EMBOSS/programs/html/eseqboot.html
 share/doc/EMBOSS/programs/html/est2genome.html
 share/doc/EMBOSS/programs/html/etandem.html
 share/doc/EMBOSS/programs/html/extractseq.html
+share/doc/EMBOSS/programs/html/factor.html
 share/doc/EMBOSS/programs/html/findkm.html
 share/doc/EMBOSS/programs/html/findkm0.gif
+share/doc/EMBOSS/programs/html/fitch.html
 share/doc/EMBOSS/programs/html/freak.html
 share/doc/EMBOSS/programs/html/fuzznuc.html
 share/doc/EMBOSS/programs/html/fuzzpro.html
 share/doc/EMBOSS/programs/html/fuzztran.html
 share/doc/EMBOSS/programs/html/garnier.html
 share/doc/EMBOSS/programs/html/geecee.html
+share/doc/EMBOSS/programs/html/gendist.html
 share/doc/EMBOSS/programs/html/gene_finding_group.html
 share/doc/EMBOSS/programs/html/getorf.html
 share/doc/EMBOSS/programs/html/groups.html
@@ -728,16 +777,20 @@ share/doc/EMBOSS/programs/html/index.html
 share/doc/EMBOSS/programs/html/infoseq.html
 share/doc/EMBOSS/programs/html/isochore.html
 share/doc/EMBOSS/programs/html/isochore0.gif
+share/doc/EMBOSS/programs/html/kitsch.html
 share/doc/EMBOSS/programs/html/lindna.html
 share/doc/EMBOSS/programs/html/maskfeat.html
 share/doc/EMBOSS/programs/html/maskseq.html
 share/doc/EMBOSS/programs/html/matcher.html
 share/doc/EMBOSS/programs/html/megamerger.html
 share/doc/EMBOSS/programs/html/merger.html
+share/doc/EMBOSS/programs/html/mix.html
 share/doc/EMBOSS/programs/html/motifs_group.html
 share/doc/EMBOSS/programs/html/msbar.html
+share/doc/EMBOSS/programs/html/mse.html
 share/doc/EMBOSS/programs/html/mutation_group.html
 share/doc/EMBOSS/programs/html/needle.html
+share/doc/EMBOSS/programs/html/neighbor.html
 share/doc/EMBOSS/programs/html/new_group_group.html
 share/doc/EMBOSS/programs/html/newcpgreport.html
 share/doc/EMBOSS/programs/html/newcpgseek.html
@@ -752,6 +805,7 @@ share/doc/EMBOSS/programs/html/pasteseq.html
 share/doc/EMBOSS/programs/html/patmatdb.html
 share/doc/EMBOSS/programs/html/patmatmotifs.html
 share/doc/EMBOSS/programs/html/pattern_matching_group.html
+share/doc/EMBOSS/programs/html/penny.html
 share/doc/EMBOSS/programs/html/pepcoil.html
 share/doc/EMBOSS/programs/html/pepinfo.html
 share/doc/EMBOSS/programs/html/pepinfo1.gif
@@ -784,6 +838,7 @@ share/doc/EMBOSS/programs/html/profit.html
 share/doc/EMBOSS/programs/html/prophecy.html
 share/doc/EMBOSS/programs/html/prophet.html
 share/doc/EMBOSS/programs/html/prosextract.html
+share/doc/EMBOSS/programs/html/protdist.html
 share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html
 share/doc/EMBOSS/programs/html/protein_sequence_features_group.html
 share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html
@@ -793,11 +848,13 @@ share/doc/EMBOSS/programs/html/redata.html
 share/doc/EMBOSS/programs/html/reformatting_group.html
 share/doc/EMBOSS/programs/html/remap.html
 share/doc/EMBOSS/programs/html/repeats_group.html
+share/doc/EMBOSS/programs/html/restml.html
 share/doc/EMBOSS/programs/html/restrict.html
 share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
 share/doc/EMBOSS/programs/html/revseq.html
 share/doc/EMBOSS/programs/html/secondary_structure_group.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
@@ -830,6 +887,8 @@ share/doc/EMBOSS/programs/html/tfm.html
 share/doc/EMBOSS/programs/html/tfscan.html
 share/doc/EMBOSS/programs/html/tmap.html
 share/doc/EMBOSS/programs/html/tmap0.gif
+share/doc/EMBOSS/programs/html/topo.gif
+share/doc/EMBOSS/programs/html/topo.html
 share/doc/EMBOSS/programs/html/transcription_group.html
 share/doc/EMBOSS/programs/html/transeq.html
 share/doc/EMBOSS/programs/html/translation_group.html
@@ -853,10 +912,15 @@ share/doc/EMBOSS/programs/text/chaos.txt
 share/doc/EMBOSS/programs/text/checktrans.txt
 share/doc/EMBOSS/programs/text/chips.txt
 share/doc/EMBOSS/programs/text/cirdna.txt
+share/doc/EMBOSS/programs/text/clique.txt
 share/doc/EMBOSS/programs/text/codcmp.txt
+share/doc/EMBOSS/programs/text/coderet.txt
 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/contml.txt
+share/doc/EMBOSS/programs/text/contrast.txt
 share/doc/EMBOSS/programs/text/cpgplot.txt
 share/doc/EMBOSS/programs/text/cpgreport.txt
 share/doc/EMBOSS/programs/text/cusp.txt
@@ -869,39 +933,79 @@ share/doc/EMBOSS/programs/text/dbigcg.txt
 share/doc/EMBOSS/programs/text/descseq.txt
 share/doc/EMBOSS/programs/text/diffseq.txt
 share/doc/EMBOSS/programs/text/digest.txt
+share/doc/EMBOSS/programs/text/dnacomp.txt
+share/doc/EMBOSS/programs/text/dnadist.txt
+share/doc/EMBOSS/programs/text/dnainvar.txt
+share/doc/EMBOSS/programs/text/dnaml.txt
+share/doc/EMBOSS/programs/text/dnamlk.txt
+share/doc/EMBOSS/programs/text/dnapars.txt
+share/doc/EMBOSS/programs/text/dnapenny.txt
+share/doc/EMBOSS/programs/text/dollop.txt
+share/doc/EMBOSS/programs/text/dolpenny.txt
 share/doc/EMBOSS/programs/text/dotmatcher.txt
 share/doc/EMBOSS/programs/text/dotpath.txt
 share/doc/EMBOSS/programs/text/dottup.txt
 share/doc/EMBOSS/programs/text/dreg.txt
+share/doc/EMBOSS/programs/text/eclique.txt
+share/doc/EMBOSS/programs/text/econsense.txt
+share/doc/EMBOSS/programs/text/econtml.txt
+share/doc/EMBOSS/programs/text/econtrast.txt
+share/doc/EMBOSS/programs/text/ednacomp.txt
+share/doc/EMBOSS/programs/text/ednadist.txt
+share/doc/EMBOSS/programs/text/ednainvar.txt
+share/doc/EMBOSS/programs/text/ednaml.txt
+share/doc/EMBOSS/programs/text/ednamlk.txt
+share/doc/EMBOSS/programs/text/ednapars.txt
+share/doc/EMBOSS/programs/text/ednapenny.txt
+share/doc/EMBOSS/programs/text/edollop.txt
+share/doc/EMBOSS/programs/text/edolpenny.txt
+share/doc/EMBOSS/programs/text/efactor.txt
+share/doc/EMBOSS/programs/text/efitch.txt
+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/emix.txt
 share/doc/EMBOSS/programs/text/emma.txt
 share/doc/EMBOSS/programs/text/emowse.txt
+share/doc/EMBOSS/programs/text/eneighbor.txt
 share/doc/EMBOSS/programs/text/entret.txt
+share/doc/EMBOSS/programs/text/epenny.txt
+share/doc/EMBOSS/programs/text/eprotdist.txt
+share/doc/EMBOSS/programs/text/eprotpars.txt
 share/doc/EMBOSS/programs/text/equicktandem.txt
+share/doc/EMBOSS/programs/text/erestml.txt
+share/doc/EMBOSS/programs/text/eseqboot.txt
 share/doc/EMBOSS/programs/text/est2genome.txt
 share/doc/EMBOSS/programs/text/etandem.txt
 share/doc/EMBOSS/programs/text/extractseq.txt
+share/doc/EMBOSS/programs/text/factor.txt
 share/doc/EMBOSS/programs/text/findkm.txt
+share/doc/EMBOSS/programs/text/fitch.txt
 share/doc/EMBOSS/programs/text/freak.txt
 share/doc/EMBOSS/programs/text/fuzznuc.txt
 share/doc/EMBOSS/programs/text/fuzzpro.txt
 share/doc/EMBOSS/programs/text/fuzztran.txt
 share/doc/EMBOSS/programs/text/garnier.txt
 share/doc/EMBOSS/programs/text/geecee.txt
+share/doc/EMBOSS/programs/text/gendist.txt
 share/doc/EMBOSS/programs/text/getorf.txt
 share/doc/EMBOSS/programs/text/helixturnhelix.txt
 share/doc/EMBOSS/programs/text/iep.txt
 share/doc/EMBOSS/programs/text/infoseq.txt
 share/doc/EMBOSS/programs/text/isochore.txt
+share/doc/EMBOSS/programs/text/kitsch.txt
 share/doc/EMBOSS/programs/text/lindna.txt
 share/doc/EMBOSS/programs/text/maskfeat.txt
 share/doc/EMBOSS/programs/text/maskseq.txt
 share/doc/EMBOSS/programs/text/matcher.txt
 share/doc/EMBOSS/programs/text/megamerger.txt
 share/doc/EMBOSS/programs/text/merger.txt
+share/doc/EMBOSS/programs/text/mix.txt
 share/doc/EMBOSS/programs/text/msbar.txt
+share/doc/EMBOSS/programs/text/mse.txt
 share/doc/EMBOSS/programs/text/needle.txt
+share/doc/EMBOSS/programs/text/neighbor.txt
 share/doc/EMBOSS/programs/text/newcpgreport.txt
 share/doc/EMBOSS/programs/text/newcpgseek.txt
 share/doc/EMBOSS/programs/text/newseq.txt
@@ -913,6 +1017,7 @@ share/doc/EMBOSS/programs/text/palindrome.txt
 share/doc/EMBOSS/programs/text/pasteseq.txt
 share/doc/EMBOSS/programs/text/patmatdb.txt
 share/doc/EMBOSS/programs/text/patmatmotifs.txt
+share/doc/EMBOSS/programs/text/penny.txt
 share/doc/EMBOSS/programs/text/pepcoil.txt
 share/doc/EMBOSS/programs/text/pepinfo.txt
 share/doc/EMBOSS/programs/text/pepnet.txt
@@ -933,13 +1038,16 @@ share/doc/EMBOSS/programs/text/profit.txt
 share/doc/EMBOSS/programs/text/prophecy.txt
 share/doc/EMBOSS/programs/text/prophet.txt
 share/doc/EMBOSS/programs/text/prosextract.txt
+share/doc/EMBOSS/programs/text/protdist.txt
 share/doc/EMBOSS/programs/text/pscan.txt
 share/doc/EMBOSS/programs/text/rebaseextract.txt
 share/doc/EMBOSS/programs/text/redata.txt
 share/doc/EMBOSS/programs/text/remap.txt
+share/doc/EMBOSS/programs/text/restml.txt
 share/doc/EMBOSS/programs/text/restrict.txt
 share/doc/EMBOSS/programs/text/revseq.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
@@ -962,6 +1070,7 @@ share/doc/EMBOSS/programs/text/tfextract.txt
 share/doc/EMBOSS/programs/text/tfm.txt
 share/doc/EMBOSS/programs/text/tfscan.txt
 share/doc/EMBOSS/programs/text/tmap.txt
+share/doc/EMBOSS/programs/text/topo.txt
 share/doc/EMBOSS/programs/text/transeq.txt
 share/doc/EMBOSS/programs/text/trimseq.txt
 share/doc/EMBOSS/programs/text/vectorstrip.txt