Attachment 86065 Details for Bug 122437 – emboss2.diff

[patch] emboss2.diff

emboss2.diff (text/x-patch), 75.20 KB, created by Fernan Aguero on 2008-04-05 14:43:14 UTC

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Filename:

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Creator: Fernan Aguero

Created: 2008-04-05 14:43:14 UTC

Size: 75.20 KB

patch

obsolete

>diff -ruN --exclude=CVS /usr/ports/biology/emboss/Makefile emboss/Makefile
>--- /usr/ports/biology/emboss/Makefile	2008-03-24 11:54:11.000000000 -0300
>+++ emboss/Makefile	2008-04-05 10:25:43.000000000 -0300
>@@ -6,26 +6,20 @@
> #
> 
> PORTNAME=	emboss
>-PORTVERSION=	3.0.0
>-PORTREVISION=	2
>+PORTVERSION=	5.0.0
>+RELEASE=	${PORTNAME:U}-${PORTVERSION}
> CATEGORIES=	biology
> MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
>-		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}
>+DISTNAME=	${RELEASE}
>+DISTFILES=	${RELEASE}${EXTRACT_SUFX}
> DIST_SUBDIR=	${PORTNAME}
> 
>-PATCH_WRKSRC=	${WRKDIR}
>-
> MAINTAINER=	fernan@iib.unsam.edu.ar
> COMMENT=	A collection of open source tools for genetic sequence analysis
> 
> BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
> 		primer3:${PORTSDIR}/biology/primer3
>-LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
>-		png.5:${PORTSDIR}/graphics/png
> 
> CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
> 
>@@ -40,21 +34,22 @@
> SUB_FILES=	pkg-message
> SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
> 
>-DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
>+DOCSDIR=	${PREFIX}/share/${PORTNAME:U}/doc
> DATADIR=	${PREFIX}/share/${PORTNAME:U}
> 
>-DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
>-CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
>+CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
> 
>-post-patch:
>-.if !defined(NOPORTDOCS)
>-.for DIR in ${DOC_DIRS}
>-	@ ${REINPLACE_CMD} -e \
>-	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
>-	  ${WRKSRC}/${DIR}/Makefile.in
>-.endfor
>+.if defined(WITHOUT_X11)
>+USE_XLIB=	yes
>+USE_MOTIF=	yes
>+LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
>+		png.5:${PORTSDIR}/graphics/png
>+CONFIGURE_ARGS+= --without-x
> .endif
> 
>+DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
>+CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
>+
> pre-install:
> 	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
> 
>diff -ruN --exclude=CVS /usr/ports/biology/emboss/distinfo emboss/distinfo
>--- /usr/ports/biology/emboss/distinfo	2006-03-31 06:43:20.000000000 -0300
>+++ emboss/distinfo	2008-04-05 10:18:24.000000000 -0300
>@@ -1,3 +1,3 @@
>-MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
>-SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
>-SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
>+MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b
>+SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
>+SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560
>diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-descr emboss/pkg-descr
>--- /usr/ports/biology/emboss/pkg-descr	2001-08-03 08:32:41.000000000 -0300
>+++ emboss/pkg-descr	2008-04-05 10:18:24.000000000 -0300
>@@ -12,12 +12,8 @@
> 
> 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.  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.
>+for licensing or other reasons. The EMBASSY packages live in the
>+biology/embassy port. 
> 
> WWW: http://www.emboss.org/
> 
>diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist
>--- /usr/ports/biology/emboss/pkg-plist	2006-03-31 06:43:20.000000000 -0300
>+++ emboss/pkg-plist	2008-04-05 10:18:24.000000000 -0300
>@@ -6,6 +6,7 @@
> bin/acdtrace
> bin/acdvalid
> bin/antigenic
>+bin/backtranambig
> bin/backtranseq
> bin/banana
> bin/biosed
>@@ -43,6 +44,7 @@
> bin/dotpath
> bin/dottup
> bin/dreg
>+bin/edialign
> bin/einverted
> bin/embossdata
> bin/embossversion
>@@ -54,6 +56,7 @@
> bin/equicktandem
> bin/est2genome
> bin/etandem
>+bin/extractalign
> bin/extractfeat
> bin/extractseq
> bin/findkm
>@@ -73,6 +76,8 @@
> bin/jembossctl
> bin/lindna
> bin/listor
>+bin/makenucseq
>+bin/makeprotseq
> bin/marscan
> bin/maskfeat
> bin/maskseq
>@@ -138,11 +143,11 @@
> bin/sirna
> bin/sixpack
> bin/skipseq
>-bin/syco
> bin/splitter
> bin/stretcher
> bin/stssearch
> bin/supermatcher
>+bin/syco
> bin/tcode
> bin/textsearch
> bin/tfextract
>@@ -160,22 +165,29 @@
> bin/whichdb
> bin/wobble
> bin/wordcount
>+bin/wordfinder
> bin/wordmatch
> bin/wossname
> bin/yank
> bin/runJemboss.csh
>-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/eplplot/drivers.h
>+include/eplplot/pdf.h
>+include/eplplot/plcore.h
>+include/eplplot/plevent.h
>+include/eplplot/plplotP.h
>+include/eplplot/plxwd.h
>+include/eplplot/metadefs.h
>+include/eplplot/plConfig.h
>+include/eplplot/pldebug.h
>+include/eplplot/plplot.h
>+include/eplplot/plstrm.h
>+include/eplplot/plDevs.h
>+include/eplplot/disptab.h
>+include/eplplot/pldll.h
>+include/eplplot/plhershey-unicode.h
>+include/eplplot/ps.h
>+include/eplplot/plunicode-type1.h
>+include/eplplot/plfci-type1.h
> include/ajax.h
> include/ajarch.h
> include/ajdefine.h
>@@ -188,6 +200,7 @@
> include/ajcod.h
> include/ajdan.h
> include/ajdmx.h
>+include/ajdom.h
> include/ajdomain.h
> include/ajexcept.h
> include/ajfeat.h
>@@ -207,6 +220,7 @@
> include/ajmess.h
> include/ajnam.h
> include/ajnexus.h
>+include/ajpat.h
> include/ajpdb.h
> include/ajpdbio.h
> include/ajphylo.h
>@@ -255,716 +269,29 @@
> include/embmol.h
> include/embnmer.h
> include/embpat.h
>+include/embpatlist.h
> include/embprop.h
> include/embpdb.h
> include/embread.h
> include/embsig.h
> include/embshow.h
> include/embword.h
>-lib/libplplot.so.5
>-lib/libplplot.so
>-lib/libplplot.la
>-lib/libplplot.a
>-lib/libajax.so.3
>+lib/libeplplot.so.5
>+lib/libeplplot.so
>+lib/libeplplot.la
>+lib/libeplplot.a
>+lib/libajax.so.5
> lib/libajax.so
> lib/libajax.la
> lib/libajax.a
>-lib/libajaxg.so.3
>+lib/libajaxg.so.5
> lib/libajaxg.so
> lib/libajaxg.la
> lib/libajaxg.a
>-lib/libnucleus.so.3
>+lib/libnucleus.so.5
> lib/libnucleus.so
> lib/libnucleus.la
> lib/libnucleus.a
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
>-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
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>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainrep.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainreso.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainseqs.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainsse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ealistat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eclique.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econsense.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtrast.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednacomp.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednadist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednainvar.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednaml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednamlk.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/egendist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmbuild.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmcalibrate.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmconvert.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmemit.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmfetch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmindex.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmpfam.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmsearch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ekitsch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emix.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emnu.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eneighbor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotdist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotpars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/erestml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eseqboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/esim4.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontrast.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdiscboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnacomp.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnadist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnainvar.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnaml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamlk.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamove.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdollop.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolmove.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolpenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawgram.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawtree.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffactor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffitch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fneighbor.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpenny.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fproml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpromlk.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotdist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotpars.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestdist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fretree.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqboot.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqbootall.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedist.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedistpair.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
>-%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
>-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
>-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
>-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
>-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
> %%DATADIR%%/plstnd5.fnt
> %%DATADIR%%/plxtnd5.fnt
> %%DATADIR%%/acd/needle.acd
>@@ -977,6 +304,8 @@
> %%DATADIR%%/acd/nthseq.acd
> %%DATADIR%%/acd/octanol.acd
> %%DATADIR%%/acd/oddcomp.acd
>+%%DATADIR%%/acd/origsplitter.acd
>+%%DATADIR%%/acd/origunion.acd
> %%DATADIR%%/acd/palindrome.acd
> %%DATADIR%%/acd/pasteseq.acd
> %%DATADIR%%/acd/patmatdb.acd
>@@ -1010,8 +339,8 @@
> %%DATADIR%%/acd/redata.acd
> %%DATADIR%%/acd/remap.acd
> %%DATADIR%%/acd/restover.acd
>-%%DATADIR%%/acd/revseq.acd
> %%DATADIR%%/acd/restrict.acd
>+%%DATADIR%%/acd/revseq.acd
> %%DATADIR%%/acd/seealso.acd
> %%DATADIR%%/acd/seqinfo.acd
> %%DATADIR%%/acd/seqmatchall.acd
>@@ -1057,11 +386,13 @@
> %%DATADIR%%/acd/whichdb.acd
> %%DATADIR%%/acd/wobble.acd
> %%DATADIR%%/acd/wordcount.acd
>+%%DATADIR%%/acd/wordfinder.acd
> %%DATADIR%%/acd/wordmatch.acd
> %%DATADIR%%/acd/wossname.acd
> %%DATADIR%%/acd/yank.acd
> %%DATADIR%%/acd/codes.english
> %%DATADIR%%/acd/groups.standard
>+%%DATADIR%%/acd/keywords.standard
> %%DATADIR%%/acd/knowntypes.standard
> %%DATADIR%%/acd/sections.standard
> %%DATADIR%%/acd/variables.standard
>@@ -1077,11 +408,12 @@
> %%DATADIR%%/acd/ajfeatest.acd
> %%DATADIR%%/acd/ajtest.acd
> %%DATADIR%%/acd/antigenic.acd
>+%%DATADIR%%/acd/backtranambig.acd
> %%DATADIR%%/acd/backtranseq.acd
>-%%DATADIR%%/acd/cai.acd
> %%DATADIR%%/acd/banana.acd
> %%DATADIR%%/acd/biosed.acd
> %%DATADIR%%/acd/btwisted.acd
>+%%DATADIR%%/acd/cai.acd
> %%DATADIR%%/acd/chaos.acd
> %%DATADIR%%/acd/charge.acd
> %%DATADIR%%/acd/checktrans.acd
>@@ -1107,6 +439,7 @@
> %%DATADIR%%/acd/dbxfasta.acd
> %%DATADIR%%/acd/dbxflat.acd
> %%DATADIR%%/acd/dbxgcg.acd
>+%%DATADIR%%/acd/dbxstat.acd
> %%DATADIR%%/acd/degapseq.acd
> %%DATADIR%%/acd/demoalign.acd
> %%DATADIR%%/acd/demofeatures.acd
>@@ -1114,6 +447,7 @@
> %%DATADIR%%/acd/demoreport.acd
> %%DATADIR%%/acd/demosequence.acd
> %%DATADIR%%/acd/demostring.acd
>+%%DATADIR%%/acd/demostringnew.acd
> %%DATADIR%%/acd/demotable.acd
> %%DATADIR%%/acd/descseq.acd
> %%DATADIR%%/acd/diffseq.acd
>@@ -1123,9 +457,9 @@
> %%DATADIR%%/acd/dotpath.acd
> %%DATADIR%%/acd/dottup.acd
> %%DATADIR%%/acd/dreg.acd
>+%%DATADIR%%/acd/edialign.acd
> %%DATADIR%%/acd/einverted.acd
> %%DATADIR%%/acd/embossdata.acd
>-%%DATADIR%%/acd/iep.acd
> %%DATADIR%%/acd/embossversion.acd
> %%DATADIR%%/acd/emma.acd
> %%DATADIR%%/acd/emowse.acd
>@@ -1136,6 +470,7 @@
> %%DATADIR%%/acd/equicktandem.acd
> %%DATADIR%%/acd/est2genome.acd
> %%DATADIR%%/acd/etandem.acd
>+%%DATADIR%%/acd/extractalign.acd
> %%DATADIR%%/acd/extractfeat.acd
> %%DATADIR%%/acd/extractseq.acd
> %%DATADIR%%/acd/findkm.acd
>@@ -1148,16 +483,17 @@
> %%DATADIR%%/acd/getorf.acd
> %%DATADIR%%/acd/giep.acd
> %%DATADIR%%/acd/helixturnhelix.acd
>-%%DATADIR%%/acd/hmoment.acd
> %%DATADIR%%/acd/histogramtest.acd
>+%%DATADIR%%/acd/hmoment.acd
>+%%DATADIR%%/acd/iep.acd
> %%DATADIR%%/acd/infoalign.acd
> %%DATADIR%%/acd/infoseq.acd
> %%DATADIR%%/acd/intconv.acd
> %%DATADIR%%/acd/isochore.acd
>-%%DATADIR%%/acd/kmrsplitter.acd
>-%%DATADIR%%/acd/kmrunion.acd
> %%DATADIR%%/acd/lindna.acd
> %%DATADIR%%/acd/listor.acd
>+%%DATADIR%%/acd/makenucseq.acd
>+%%DATADIR%%/acd/makeprotseq.acd
> %%DATADIR%%/acd/marscan.acd
> %%DATADIR%%/acd/maskfeat.acd
> %%DATADIR%%/acd/maskseq.acd
>@@ -1526,6 +862,8 @@
> %%DATADIR%%/data/Efeatures.embl
> %%DATADIR%%/data/Efeatures.emboss
> %%DATADIR%%/data/Efeatures.gff
>+%%DATADIR%%/data/Efeatures.gff3
>+%%DATADIR%%/data/Efeatures.gffprotein
> %%DATADIR%%/data/Efeatures.pir
> %%DATADIR%%/data/Efeatures.protein
> %%DATADIR%%/data/Efeatures.swiss
>@@ -1546,6 +884,8 @@
> %%DATADIR%%/data/Etags.embl
> %%DATADIR%%/data/Etags.emboss
> %%DATADIR%%/data/Etags.gff
>+%%DATADIR%%/data/Etags.gff3
>+%%DATADIR%%/data/Etags.gffprotein
> %%DATADIR%%/data/Etags.pir
> %%DATADIR%%/data/Etags.protein
> %%DATADIR%%/data/Etags.swiss
>@@ -1559,6 +899,10 @@
> %%DATADIR%%/data/Matrices.nucleotide
> %%DATADIR%%/data/Matrices.protein
> %%DATADIR%%/data/Matrices.proteinstructure
>+%%DATADIR%%/data/edialignmat
>+%%DATADIR%%/data/tp400_dna
>+%%DATADIR%%/data/tp400_prot
>+%%DATADIR%%/data/tp400_trans
> %%DATADIR%%/emboss.default.template
> %%DATADIR%%/test/data/aaindex1.test
> %%DATADIR%%/test/data/prosite.dat
>@@ -1609,6 +953,7 @@
> %%DATADIR%%/test/data/prot.ig
> %%DATADIR%%/test/data/prot.m-acedb
> %%DATADIR%%/test/data/prot.m-codata
>+%%DATADIR%%/test/data/nuc.pat
> %%DATADIR%%/test/data/prot.m-fasta
> %%DATADIR%%/test/data/prot.m-nbrf
> %%DATADIR%%/test/data/prot.m-ncbi
>@@ -1618,14 +963,20 @@
> %%DATADIR%%/test/data/prot.swiss
> %%DATADIR%%/test/data/prot.text
> %%DATADIR%%/test/data/z83307.seq
>+%%DATADIR%%/test/data/104k.nbrf
> %%DATADIR%%/test/data/aligna.dna
> %%DATADIR%%/test/data/alignapart.dna
> %%DATADIR%%/test/data/alignb.dna
> %%DATADIR%%/test/data/aligna.prot
> %%DATADIR%%/test/data/alignapart.prot
> %%DATADIR%%/test/data/alignb.prot
>+%%DATADIR%%/test/data/nucseq.pat
>+%%DATADIR%%/test/data/nucsimple.pat
> %%DATADIR%%/test/data/tranalign.pep
> %%DATADIR%%/test/data/tranalign.seq
>+%%DATADIR%%/test/data/vtest.seq
>+%%DATADIR%%/test/data/opsd.msf
>+%%DATADIR%%/test/data/untrimmed.seq
> %%DATADIR%%/test/embl/acnum.hit
> %%DATADIR%%/test/embl/acnum.trg
> %%DATADIR%%/test/embl/division.lkp
>@@ -1670,22 +1021,6 @@
> %%DATADIR%%/test/genbank/gbsts1.seq
> %%DATADIR%%/test/genbank/gbvrl1.seq
> %%DATADIR%%/test/genbank/gbvrt.seq
>-%%DATADIR%%/test/gb/acnum.hit
>-%%DATADIR%%/test/gb/acnum.trg
>-%%DATADIR%%/test/gb/division.lkp
>-%%DATADIR%%/test/gb/entrynam.idx
>-%%DATADIR%%/test/gb/seqvn.hit
>-%%DATADIR%%/test/gb/seqvn.trg
>-%%DATADIR%%/test/gb/des.hit
>-%%DATADIR%%/test/gb/des.trg
>-%%DATADIR%%/test/gb/keyword.hit
>-%%DATADIR%%/test/gb/keyword.trg
>-%%DATADIR%%/test/gb/taxon.hit
>-%%DATADIR%%/test/gb/taxon.trg
>-%%DATADIR%%/test/gb/ba.ref
>-%%DATADIR%%/test/gb/ba.seq
>-%%DATADIR%%/test/gb/htg.ref
>-%%DATADIR%%/test/gb/htg.seq
> %%DATADIR%%/test/pir/acnum.hit
> %%DATADIR%%/test/pir/acnum.trg
> %%DATADIR%%/test/pir/division.lkp
>@@ -1745,16 +1080,457 @@
> %%DATADIR%%/test/swnew/keyword.trg
> %%DATADIR%%/test/swnew/taxon.hit
> %%DATADIR%%/test/swnew/taxon.trg
>-%%DATADIR%%/test/swnew/new_seq.dat
>-%%DATADIR%%/test/swnew/upd_ann.dat
>-%%DATADIR%%/test/swnew/upd_seq.dat
>-%%DATADIR%%/test/wormpep/wormpep
>-%%DATADIR%%/test/wormpep/acnum.hit
>-%%DATADIR%%/test/wormpep/acnum.trg
>-%%DATADIR%%/test/wormpep/division.lkp
>-%%DATADIR%%/test/wormpep/entrynam.idx
>-%%DATADIR%%/test/wormpep/des.hit
>-%%DATADIR%%/test/wormpep/des.trg
>+%%DATADIR%%/test/swnew/trembl.dat
>+%%DATADIR%%/test/testdb/testdb.fasta
>+%%DATADIR%%/test/testdb/acnum.hit
>+%%DATADIR%%/test/testdb/acnum.trg
>+%%DATADIR%%/test/testdb/division.lkp
>+%%DATADIR%%/test/testdb/entrynam.idx
>+%%DATADIR%%/test/testdb/des.hit
>+%%DATADIR%%/test/testdb/des.trg
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
>+%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/lindna.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/listor.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/makenucseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/makeprotseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/marscan.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/maskfeat.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/maskseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/matcher.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/megamerger.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/menus_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/merger.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/msbar.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/mwcontam.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/mwfilter.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/needle.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newcpgreport.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newcpgseek.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/noreturn.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/notseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nthseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_2d_structure_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_codon_usage_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_codon_usage_nucleic_gene_finding_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_composition_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_cpg_islands_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_gene_finding_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_motifs_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_mutation_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_primers_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_profiles_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_repeats_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_restriction_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/octanol.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_transcription_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_translation_group.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/oddcomp.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/palindrome.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pasteseq.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/patmatdb.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/patmatmotifs.html
>+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepcoil.html
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>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dan.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcopy.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cusp.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutgextract.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiblast.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/edialign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
>+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
>+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
>+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
>+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
> %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/DragTree.html
> %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html
> %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html
>@@ -1913,6 +1689,7 @@
> %%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/MultiTextField.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
>@@ -2006,28 +1783,31 @@
> %%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 include/eplplot
>+@dirrm include
> @dirrm %%DATADIR%%/acd
>-@dirrm %%DATADIR%%/data/AAINDEX
>-@dirrm %%DATADIR%%/data/CODONS
>-@dirrm %%DATADIR%%/data/REBASE
>-@dirrm %%DATADIR%%/data/PRINTS
>-@dirrm %%DATADIR%%/data/PROSITE
>+@dirrmtry %%DATADIR%%/data/AAINDEX
>+@dirrmtry %%DATADIR%%/data/CODONS
>+@dirrmtry %%DATADIR%%/data/REBASE
>+@dirrmtry %%DATADIR%%/data/PRINTS
>+@dirrmtry %%DATADIR%%/data/PROSITE
> @dirrmtry %%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/testdb
> @dirrm %%DATADIR%%/test
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/html/emboss/apps
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/html/emboss
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/html
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%
> @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
>@@ -2067,5 +1847,4 @@
> @dirrmtry bin
> @dirrmtry include
> @dirrmtry lib
>-@dirrmtry share/doc
> @dirrmtry share

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Attachments on bug 122437: 86064 | 86065