Upgrade to 1.5.0

PR:		21108
Submitted by:	Johann Visagie <johann@egenetics.com>

4 files changed, 113 insertions, 66 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index e246f10d8e31..a4309edff758 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,9 +6,10 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.4.0
+PORTVERSION=	1.5.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/
+MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
+		ftp://ftp.no.embnet.org/pub/EMBOSS/
 DISTNAME=	EMBOSS-${PORTVERSION}
 
 MAINTAINER=	johann@egenetics.com
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index f42c83e49367..21c791941839 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1 +1 @@
-MD5 (EMBOSS-1.4.0.tar.gz) = ba096906cc10d0badbc1c479e61926c9
+MD5 (EMBOSS-1.5.0.tar.gz) = 633d21e6daf080ed0deed159d21fe920
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
index f14bff524b5a..a34183b481ce 100644
--- a/biology/emboss/pkg-message
+++ b/biology/emboss/pkg-message
@@ -19,4 +19,7 @@ system-wide emboss.default.
 Further EMBOSS documentation is available at:
 	http://www.uk.embnet.org/Software/EMBOSS/Doc/
 
+The EMBOSS administrator's guide is available in various formats at:
+	ftp://ftp.no.embnet.org/pub/EMBOSS-extras/
+
 --------------------------------------------------------------------------
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index b62a97f96d93..17f29251c4bd 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -2,6 +2,7 @@ bin/acdc
 bin/antigenic
 bin/backtranseq
 bin/banana
+bin/btwisted
 bin/chaos
 bin/checktrans
 bin/chips
@@ -25,10 +26,11 @@ bin/dotmatcher
 bin/dotpath
 bin/dottup
 bin/dreg
-bin/einverted
 bin/iep
+bin/einverted
 bin/embossdata
 bin/emma
+bin/emowse
 bin/equicktandem
 bin/est2genome
 bin/etandem
@@ -107,8 +109,8 @@ bin/stssearch
 bin/supermatcher
 bin/syco
 bin/textsearch
-bin/tfextract
 bin/tfm
+bin/tfextract
 bin/tfscan
 bin/tmap
 bin/transeq
@@ -132,14 +134,13 @@ lib/libajaxg.a
 lib/libnucleus.so.1
 lib/libnucleus.so
 lib/libnucleus.a
-share/doc/EMBOSS/manuals/Makefile
-share/doc/EMBOSS/manuals/Makefile.am
-share/doc/EMBOSS/manuals/Makefile.in
-share/doc/EMBOSS/manuals/Makefile.in.orig
-share/doc/EMBOSS/programs/html/Makefile
-share/doc/EMBOSS/programs/html/Makefile.am
-share/doc/EMBOSS/programs/html/Makefile.in
-share/doc/EMBOSS/programs/html/Makefile.in.orig
+share/doc/EMBOSS/manuals/admin.sty
+share/doc/EMBOSS/manuals/admin.tex
+share/doc/EMBOSS/programs/html/SITE-DIRECTED.html
+share/doc/EMBOSS/programs/html/alignment_global_group.html
+share/doc/EMBOSS/programs/html/alignment_group.html
+share/doc/EMBOSS/programs/html/alignment_local_group.html
+share/doc/EMBOSS/programs/html/alignment_multiple_group.html
 share/doc/EMBOSS/programs/html/antigenic.html
 share/doc/EMBOSS/programs/html/backtranseq.html
 share/doc/EMBOSS/programs/html/banana.html
@@ -148,20 +149,30 @@ 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/codcmp.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/cpgplot.html
+share/doc/EMBOSS/programs/html/cpg_islands_group.html
 share/doc/EMBOSS/programs/html/cpgreport.html
 share/doc/EMBOSS/programs/html/cusp.html
 share/doc/EMBOSS/programs/html/cutseq.html
 share/doc/EMBOSS/programs/html/dan.html
+share/doc/EMBOSS/programs/html/database_entry_extraction_group.html
+share/doc/EMBOSS/programs/html/database_indexing_group.html
+share/doc/EMBOSS/programs/html/database_information_group.html
 share/doc/EMBOSS/programs/html/dbiblast.html
 share/doc/EMBOSS/programs/html/dbifasta.html
-share/doc/EMBOSS/programs/html/dbigcg.html
 share/doc/EMBOSS/programs/html/dbiflat.html
+share/doc/EMBOSS/programs/html/dbigcg.html
 share/doc/EMBOSS/programs/html/descseq.html
 share/doc/EMBOSS/programs/html/diffseq.html
 share/doc/EMBOSS/programs/html/digest.html
+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/dotmatcher.html
 share/doc/EMBOSS/programs/html/dotpath.html
 share/doc/EMBOSS/programs/html/dottup.html
@@ -169,6 +180,7 @@ share/doc/EMBOSS/programs/html/dreg.html
 share/doc/EMBOSS/programs/html/einverted.html
 share/doc/EMBOSS/programs/html/embossdata.html
 share/doc/EMBOSS/programs/html/emma.html
+share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
 share/doc/EMBOSS/programs/html/equicktandem.html
 share/doc/EMBOSS/programs/html/est2genome.html
 share/doc/EMBOSS/programs/html/etandem.html
@@ -178,11 +190,15 @@ 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/garnier.html
+share/doc/EMBOSS/programs/html/gene_finding_group.html
 share/doc/EMBOSS/programs/html/getorf.html
+share/doc/EMBOSS/programs/html/groups.html
 share/doc/EMBOSS/programs/html/helixturnhelix.html
+share/doc/EMBOSS/programs/html/hydropathy_group.html
 share/doc/EMBOSS/programs/html/iep.html
+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/lindna.html
@@ -191,8 +207,11 @@ 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/motifs_group.html
 share/doc/EMBOSS/programs/html/msbar.html
+share/doc/EMBOSS/programs/html/mutation_group.html
 share/doc/EMBOSS/programs/html/needle.html
+share/doc/EMBOSS/programs/html/new_group_group.html
 share/doc/EMBOSS/programs/html/newcpgreport.html
 share/doc/EMBOSS/programs/html/newcpgseek.html
 share/doc/EMBOSS/programs/html/newseq.html
@@ -204,6 +223,7 @@ share/doc/EMBOSS/programs/html/palindrome.html
 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/pepcoil.html
 share/doc/EMBOSS/programs/html/pepinfo.html
 share/doc/EMBOSS/programs/html/pepnet.html
@@ -212,60 +232,102 @@ share/doc/EMBOSS/programs/html/pepwheel.html
 share/doc/EMBOSS/programs/html/pepwindow.html
 share/doc/EMBOSS/programs/html/pepwindowall.html
 share/doc/EMBOSS/programs/html/plotorf.html
-share/doc/EMBOSS/programs/html/polydot.html
 share/doc/EMBOSS/programs/html/preg.html
+share/doc/EMBOSS/programs/html/polydot.html
 share/doc/EMBOSS/programs/html/prettyplot.html
 share/doc/EMBOSS/programs/html/prettyseq.html
 share/doc/EMBOSS/programs/html/prima.html
+share/doc/EMBOSS/programs/html/primers_group.html
 share/doc/EMBOSS/programs/html/primersearch.html
 share/doc/EMBOSS/programs/html/printsextract.html
+share/doc/EMBOSS/programs/html/profiles_group.html
 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/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
 share/doc/EMBOSS/programs/html/pscan.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
 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/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/seqmatchall.html
 share/doc/EMBOSS/programs/html/seqret.html
 share/doc/EMBOSS/programs/html/seqretall.html
 share/doc/EMBOSS/programs/html/seqretset.html
+share/doc/EMBOSS/programs/html/sequence_comparison_group.html
+share/doc/EMBOSS/programs/html/sequence_composition_group.html
+share/doc/EMBOSS/programs/html/sequence_display_group.html
+share/doc/EMBOSS/programs/html/sequence_editing_group.html
 share/doc/EMBOSS/programs/html/showdb.html
+share/doc/EMBOSS/programs/html/sequence_information_group.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/silent.html
+share/doc/EMBOSS/programs/html/site_directed_mutagenesis_group.html
 share/doc/EMBOSS/programs/html/splitter.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/syco.html
+share/doc/EMBOSS/programs/html/text_search_group.html
 share/doc/EMBOSS/programs/html/textsearch.html
 share/doc/EMBOSS/programs/html/tfextract.html
 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/transeq.html
+share/doc/EMBOSS/programs/html/transcription_group.html
+share/doc/EMBOSS/programs/html/translation_group.html
 share/doc/EMBOSS/programs/html/trimseq.html
+share/doc/EMBOSS/programs/html/utilities_group.html
+share/doc/EMBOSS/programs/html/utilities_help_group.html
+share/doc/EMBOSS/programs/html/utilities_keyword_search_group.html
 share/doc/EMBOSS/programs/html/vectorstrip.html
 share/doc/EMBOSS/programs/html/water.html
 share/doc/EMBOSS/programs/html/wobble.html
 share/doc/EMBOSS/programs/html/wordcount.html
 share/doc/EMBOSS/programs/html/wordmatch.html
 share/doc/EMBOSS/programs/html/wossname.html
-share/doc/EMBOSS/programs/text/Makefile
-share/doc/EMBOSS/programs/text/Makefile.am
-share/doc/EMBOSS/programs/text/Makefile.in
-share/doc/EMBOSS/programs/text/Makefile.in.orig
+share/doc/EMBOSS/programs/html/banana0.gif
+share/doc/EMBOSS/programs/html/chaos0.gif
+share/doc/EMBOSS/programs/html/cpgplot0.gif
+share/doc/EMBOSS/programs/html/dotmatcher0.gif
+share/doc/EMBOSS/programs/html/dottup0.gif
+share/doc/EMBOSS/programs/html/emboss_icon.gif
+share/doc/EMBOSS/programs/html/findkm0.gif
+share/doc/EMBOSS/programs/html/isochore0.gif
+share/doc/EMBOSS/programs/html/octanol0.gif
+share/doc/EMBOSS/programs/html/pepinfo1.gif
+share/doc/EMBOSS/programs/html/pepinfo2.gif
+share/doc/EMBOSS/programs/html/pepnet0.gif
+share/doc/EMBOSS/programs/html/pepwheel0.gif
+share/doc/EMBOSS/programs/html/pepwindow0.gif
+share/doc/EMBOSS/programs/html/pepwindowall0.gif
+share/doc/EMBOSS/programs/html/plotorf0.gif
+share/doc/EMBOSS/programs/html/polydot0.gif
+share/doc/EMBOSS/programs/html/prettyplot3.gif
+share/doc/EMBOSS/programs/html/prettyplot4.gif
+share/doc/EMBOSS/programs/html/syco0.gif
+share/doc/EMBOSS/programs/html/syco1.gif
+share/doc/EMBOSS/programs/html/tmap0.gif
+share/doc/EMBOSS/programs/html/wobble0.gif
+share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt
 share/doc/EMBOSS/programs/text/antigenic.txt
 share/doc/EMBOSS/programs/text/backtranseq.txt
 share/doc/EMBOSS/programs/text/banana.txt
+share/doc/EMBOSS/programs/text/btwisted.txt
 share/doc/EMBOSS/programs/text/chaos.txt
 share/doc/EMBOSS/programs/text/checktrans.txt
 share/doc/EMBOSS/programs/text/chips.txt
@@ -283,6 +345,7 @@ share/doc/EMBOSS/programs/text/dbifasta.txt
 share/doc/EMBOSS/programs/text/dbiflat.txt
 share/doc/EMBOSS/programs/text/dbigcg.txt
 share/doc/EMBOSS/programs/text/descseq.txt
+share/doc/EMBOSS/programs/text/iep.txt
 share/doc/EMBOSS/programs/text/diffseq.txt
 share/doc/EMBOSS/programs/text/digest.txt
 share/doc/EMBOSS/programs/text/dotmatcher.txt
@@ -305,7 +368,6 @@ share/doc/EMBOSS/programs/text/garnier.txt
 share/doc/EMBOSS/programs/text/geecee.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/lindna.txt
@@ -382,15 +444,15 @@ share/doc/EMBOSS/programs/text/wobble.txt
 share/doc/EMBOSS/programs/text/wordcount.txt
 share/doc/EMBOSS/programs/text/wordmatch.txt
 share/doc/EMBOSS/programs/text/wossname.txt
-share/doc/EMBOSS/tutorials/Makefile
-share/doc/EMBOSS/tutorials/Makefile.am
-share/doc/EMBOSS/tutorials/Makefile.in
-share/doc/EMBOSS/tutorials/Makefile.in.orig
+share/doc/EMBOSS/tutorials/biblio.bib
+share/doc/EMBOSS/tutorials/emboss_tutorial.tex
+share/doc/EMBOSS/tutorials/dottup.ps
+share/doc/EMBOSS/tutorials/pepinfo1.ps
+share/doc/EMBOSS/tutorials/pepinfo2.ps
+share/doc/EMBOSS/tutorials/plotorf.ps
+share/doc/EMBOSS/tutorials/tmap.ps
 share/EMBOSS/plstnd5.fnt
 share/EMBOSS/plxtnd5.fnt
-share/EMBOSS/acd/Makefile
-share/EMBOSS/acd/Makefile.am
-share/EMBOSS/acd/Makefile.in
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
@@ -398,13 +460,13 @@ share/EMBOSS/acd/ajtest2.acd
 share/EMBOSS/acd/antigenic.acd
 share/EMBOSS/acd/backtranseq.acd
 share/EMBOSS/acd/banana.acd
+share/EMBOSS/acd/btwisted.acd
 share/EMBOSS/acd/chaos.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/codes.english
 share/EMBOSS/acd/complex.acd
 share/EMBOSS/acd/compseq.acd
 share/EMBOSS/acd/cpgplot.acd
@@ -429,13 +491,14 @@ share/EMBOSS/acd/dotpath.acd
 share/EMBOSS/acd/dottup.acd
 share/EMBOSS/acd/dreg.acd
 share/EMBOSS/acd/einverted.acd
-share/EMBOSS/acd/emboss.default
 share/EMBOSS/acd/embossdata.acd
 share/EMBOSS/acd/emma.acd
+share/EMBOSS/acd/emowse.acd
 share/EMBOSS/acd/entrails.acd
-share/EMBOSS/acd/etandem.acd
 share/EMBOSS/acd/equicktandem.acd
 share/EMBOSS/acd/est2genome.acd
+share/EMBOSS/acd/etandem.acd
+share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/extractseq.acd
 share/EMBOSS/acd/findkm.acd
 share/EMBOSS/acd/freak.acd
@@ -447,7 +510,6 @@ share/EMBOSS/acd/geecee.acd
 share/EMBOSS/acd/getorf.acd
 share/EMBOSS/acd/helixturnhelix.acd
 share/EMBOSS/acd/histogramtest.acd
-share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
 share/EMBOSS/acd/lindna.acd
@@ -482,6 +544,7 @@ share/EMBOSS/acd/plplottest.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
+share/EMBOSS/acd/tfm.acd
 share/EMBOSS/acd/prettyseq.acd
 share/EMBOSS/acd/prima.acd
 share/EMBOSS/acd/primersearch.acd
@@ -522,7 +585,6 @@ share/EMBOSS/acd/stssearch.acd
 share/EMBOSS/acd/supermatcher.acd
 share/EMBOSS/acd/syco.acd
 share/EMBOSS/acd/testplot.acd
-share/EMBOSS/acd/tfm.acd
 share/EMBOSS/acd/textsearch.acd
 share/EMBOSS/acd/tfextract.acd
 share/EMBOSS/acd/tfscan.acd
@@ -536,6 +598,8 @@ share/EMBOSS/acd/wobble.acd
 share/EMBOSS/acd/wordcount.acd
 share/EMBOSS/acd/wordmatch.acd
 share/EMBOSS/acd/wossname.acd
+share/EMBOSS/acd/codes.english
+share/EMBOSS/acd/emboss.default
 share/EMBOSS/data/CODONS/Eacc.cut
 share/EMBOSS/data/CODONS/Eadenovirus5.cut
 share/EMBOSS/data/CODONS/Eadenovirus7.cut
@@ -687,9 +751,6 @@ share/EMBOSS/data/CODONS/Eyscmt.cut
 share/EMBOSS/data/CODONS/Eysp.cut
 share/EMBOSS/data/CODONS/Ezebrafish.cut
 share/EMBOSS/data/CODONS/Ezma.cut
-share/EMBOSS/data/CODONS/Makefile
-share/EMBOSS/data/CODONS/Makefile.am
-share/EMBOSS/data/CODONS/Makefile.in
 share/EMBOSS/data/REBASE/dummyfile
 share/EMBOSS/data/PRINTS/dummyfile
 share/EMBOSS/data/PROSITE/dummyfile
@@ -782,13 +843,16 @@ share/EMBOSS/data/Eaa_acc_surface.dat
 share/EMBOSS/data/Eaa_hydropathy.dat
 share/EMBOSS/data/Eaa_properties.dat
 share/EMBOSS/data/Eamino.dat
+share/EMBOSS/data/Eangles.dat
 share/EMBOSS/data/Eangles_tri.dat
 share/EMBOSS/data/Eantigenic.dat
 share/EMBOSS/data/Ebases.iub
 share/EMBOSS/data/Edayhoff.freq
 share/EMBOSS/data/Edna.melt
+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/Enakai.dat
@@ -800,13 +864,7 @@ share/EMBOSS/data/Esig.pro
 share/EMBOSS/data/Etags.embl
 share/EMBOSS/data/Etags.gff
 share/EMBOSS/data/Ewhite-wimley.dat
-share/EMBOSS/data/Makefile
-share/EMBOSS/data/Makefile.am
-share/EMBOSS/data/Makefile.in
 share/EMBOSS/data/embossre.equ
-share/EMBOSS/test/data/Makefile
-share/EMBOSS/test/data/Makefile.am
-share/EMBOSS/test/data/Makefile.in
 share/EMBOSS/test/data/dna.acedb
 share/EMBOSS/test/data/dna.aln
 share/EMBOSS/test/data/dna.asn1
@@ -849,13 +907,6 @@ share/EMBOSS/test/data/prot.nbrf
 share/EMBOSS/test/data/prot.ncbi
 share/EMBOSS/test/data/prot.swiss
 share/EMBOSS/test/data/prot.text
-share/EMBOSS/test/embl/Makefile
-share/EMBOSS/test/embl/Makefile.am
-share/EMBOSS/test/embl/Makefile.in
-share/EMBOSS/test/embl/acnum.hit
-share/EMBOSS/test/embl/acnum.trg
-share/EMBOSS/test/embl/division.lkp
-share/EMBOSS/test/embl/entrynam.idx
 share/EMBOSS/test/embl/est.dat
 share/EMBOSS/test/embl/hum1.dat
 share/EMBOSS/test/embl/inv.dat
@@ -863,9 +914,10 @@ share/EMBOSS/test/embl/pro.dat
 share/EMBOSS/test/embl/rod.dat
 share/EMBOSS/test/embl/vrl.dat
 share/EMBOSS/test/embl/vrt.dat
-share/EMBOSS/test/pir/Makefile
-share/EMBOSS/test/pir/Makefile.am
-share/EMBOSS/test/pir/Makefile.in
+share/EMBOSS/test/embl/acnum.hit
+share/EMBOSS/test/embl/acnum.trg
+share/EMBOSS/test/embl/division.lkp
+share/EMBOSS/test/embl/entrynam.idx
 share/EMBOSS/test/pir/pir1.header
 share/EMBOSS/test/pir/pir1.names
 share/EMBOSS/test/pir/pir1.numbers
@@ -890,32 +942,23 @@ share/EMBOSS/test/pir/pir4.numbers
 share/EMBOSS/test/pir/pir4.offset
 share/EMBOSS/test/pir/pir4.ref
 share/EMBOSS/test/pir/pir4.seq
-share/EMBOSS/test/swiss/Makefile
-share/EMBOSS/test/swiss/Makefile.am
-share/EMBOSS/test/swiss/Makefile.in
+share/EMBOSS/test/swiss/seq.dat
 share/EMBOSS/test/swiss/acnum.hit
 share/EMBOSS/test/swiss/acnum.trg
 share/EMBOSS/test/swiss/division.lkp
 share/EMBOSS/test/swiss/entrynam.idx
-share/EMBOSS/test/swiss/seq.dat
-share/EMBOSS/test/swnew/Makefile
-share/EMBOSS/test/swnew/Makefile.am
-share/EMBOSS/test/swnew/Makefile.in
+share/EMBOSS/test/swnew/new_seq.dat
+share/EMBOSS/test/swnew/upd_ann.dat
+share/EMBOSS/test/swnew/upd_seq.dat
 share/EMBOSS/test/swnew/acnum.hit
 share/EMBOSS/test/swnew/acnum.trg
 share/EMBOSS/test/swnew/division.lkp
 share/EMBOSS/test/swnew/entrynam.idx
-share/EMBOSS/test/swnew/new_seq.dat
-share/EMBOSS/test/swnew/upd_ann.dat
-share/EMBOSS/test/swnew/upd_seq.dat
-share/EMBOSS/test/wormpep/Makefile
-share/EMBOSS/test/wormpep/Makefile.am
-share/EMBOSS/test/wormpep/Makefile.in
+share/EMBOSS/test/wormpep/wormpep
 share/EMBOSS/test/wormpep/acnum.hit
 share/EMBOSS/test/wormpep/acnum.trg
 share/EMBOSS/test/wormpep/division.lkp
 share/EMBOSS/test/wormpep/entrynam.idx
-share/EMBOSS/test/wormpep/wormpep
 @dirrm share/doc/EMBOSS/manuals
 @dirrm share/doc/EMBOSS/programs/html
 @dirrm share/doc/EMBOSS/programs/text