Date: Fri, 4 Apr 2008 04:53:54 GMT From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/122437: [maintainer] update emboss and embassy to v5.0.0 Message-ID: <200804040453.m344rssx099126@www.freebsd.org> Resent-Message-ID: <200804040500.m3450CYN076762@freefall.freebsd.org>
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>Number: 122437
>Category: ports
>Synopsis: [maintainer] update emboss and embassy to v5.0.0
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Fri Apr 04 05:00:12 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: 6.3
>Organization:
IIB-UNSAM
>Environment:
>Description:
update to latest release.
>How-To-Repeat:
>Fix:
diff -ruN --exclude=CVS /usr/ports/biology/emboss/Makefile emboss/Makefile
--- /usr/ports/biology/emboss/Makefile Mon Jun 18 20:28:09 2007
+++ emboss/Makefile Fri Aug 17 12:05:27 2007
@@ -6,26 +6,20 @@
#
PORTNAME= emboss
-PORTVERSION= 3.0.0
-PORTREVISION= 1
+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:${PORTSDIR}/graphics/png
CONFLICTS= qmail-ldap-[0-9]* digest-[0-9]*
@@ -41,20 +35,21 @@
SUB_FILES= pkg-message
SUB_LIST= PREFIX=${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 Fri Mar 31 06:43:20 2006
+++ emboss/distinfo Fri Jul 20 23:38:22 2007
@@ -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 Fri Aug 3 08:32:41 2001
+++ emboss/pkg-descr Wed Feb 7 11:49:31 2007
@@ -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 Fri Mar 31 06:43:20 2006
+++ emboss/pkg-plist Fri Aug 17 11:07:25 2007
@@ -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
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
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-%%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
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-%%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
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%%DATADIR%%/plstnd5.fnt
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@@ -977,6 +304,8 @@
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+%%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
Patch attached with submission follows:
diff -ruN --exclude CVS /usr/ports/biology/embassy/Makefile embassy/Makefile
--- /usr/ports/biology/embassy/Makefile Mon Mar 24 11:54:11 2008
+++ embassy/Makefile Fri Aug 17 12:09:48 2007
@@ -3,23 +3,20 @@
# Date created: 1.November.2004
# Whom: Fernan Aguero <fernan@iib.unsamn.edu.ar>
#
-# $FreeBSD: ports/biology/embassy/Makefile,v 1.9 2008/03/23 16:44:05 miwi Exp $
+# $FreeBSD: ports/biology/embassy/Makefile,v 1.6 2006/03/31 09:43:21 thierry Exp $
#
PORTNAME= embassy
-PORTVERSION= 3.0.0
-PORTREVISION= 2
+PORTVERSION= 5.0.0
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/
DIST_SUBDIR= emboss
MAINTAINER= fernan@iib.unsam.edu.ar
COMMENT= A collection of contributed EMBOSS applications
-LIB_DEPENDS= nucleus.3:${PORTSDIR}/biology/emboss
+LIB_DEPENDS= nucleus.5:${PORTSDIR}/biology/emboss
PREFIX?= ${LOCALBASE}/emboss
NO_MTREE= yes
@@ -27,7 +24,9 @@
USE_ICONV= yes
USE_GMAKE= yes
GNU_CONFIGURE= yes
+USE_XLIB= yes
USE_MOTIF= yes
+USE_LDCONFIG= yes
OPTIONS= DOMAINATRIX "Protein domain apps" on \
DOMALIGN "Protein domain apps" on \
@@ -41,7 +40,8 @@
MSE "A multiple sequence screen editor" on \
MYEMBOSS "Examples for developers of EMBOSS apps" on \
PHYLIP "Phylogeny inference" on \
- TOPO "Transmembrane display" on
+ TOPO "Transmembrane display" on \
+ VIENNA "RNA folding" on
CONFIGURE_ENV+= CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
@@ -50,8 +50,8 @@
DOMAINATRIX_VERSION= 0.1.0
EMNU_VERSION= 1.05
ESIM4_VERSION= 1.0.0
-HMMER_VERSION= 2.1.1
-MEME_VERSION= 2.3.1
+HMMER_VERSION= 2.3.2
+MEME_VERSION= 0.1.0
MSE_VERSION= 1.0.0
TOPO_VERSION= 1.0.0
PHYLIP_VERSION= 3.6b
@@ -60,8 +60,10 @@
SIGNATURE_VERSION= 0.1.0
STRUCTURE_VERSION= 0.1.0
MYEMBOSS_VERSION= 3.0.0
-EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \
- DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS
+VIENNA_VERSION= 1.6
+EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP \
+ TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \
+ VIENNA
.include <bsd.port.pre.mk>
@@ -88,9 +90,6 @@
${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
fi
.endfor
-
-post-patch:
- @${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|'
do-configure:
.for app in ${APPLIST}
diff -ruN --exclude CVS /usr/ports/biology/embassy/distinfo embassy/distinfo
--- /usr/ports/biology/embassy/distinfo Fri Mar 31 06:43:21 2006
+++ embassy/distinfo Fri Aug 17 12:59:16 2007
@@ -1,39 +1,42 @@
-MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 655f6ec58e0b9dfdac111fd9481359cb
-SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 6bc374c5275dead68ef09d8273bf4d73a03bc56990e795d6eddcee4de25c12a0
-SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 349882
-MD5 (emboss/EMNU-1.05.tar.gz) = b3a7fc11e46f7166ddeec11f2fe03d9b
-SHA256 (emboss/EMNU-1.05.tar.gz) = d7261d615d6547a9824d3d9e3f82ff756c0db5786e8356bc54cc5fa0c516b26f
-SIZE (emboss/EMNU-1.05.tar.gz) = 348924
-MD5 (emboss/ESIM4-1.0.0.tar.gz) = 835393b3246eb4543a694362c6f335ff
-SHA256 (emboss/ESIM4-1.0.0.tar.gz) = f8241c9e37ccc17dbd29df2d9c90063ba7caf4e64cc5c368b6878c3aa3895620
-SIZE (emboss/ESIM4-1.0.0.tar.gz) = 384396
-MD5 (emboss/HMMER-2.1.1.tar.gz) = 382594654e45a7e8d5872b4b1016a494
-SHA256 (emboss/HMMER-2.1.1.tar.gz) = 78647dfb7841e8b52b4c3de34400c68d17a877b698956ac9a5ee5e030569cca6
-SIZE (emboss/HMMER-2.1.1.tar.gz) = 561289
-MD5 (emboss/MEME-2.3.1.tar.gz) = 6f4e516e413582268a34e91fb12e21c3
-SHA256 (emboss/MEME-2.3.1.tar.gz) = bec2c8002b8b551ef9c639bcb58633499060cd8a1bfe4754db5ed201a6a0dffa
-SIZE (emboss/MEME-2.3.1.tar.gz) = 423966
-MD5 (emboss/MSE-1.0.0.tar.gz) = 3b9810e870937ec32220b5c9fe7a83cd
-SHA256 (emboss/MSE-1.0.0.tar.gz) = ddf9092721666d64c56733d9b6d04e749957848cafa8ba4ec6eee083a0ffcab3
-SIZE (emboss/MSE-1.0.0.tar.gz) = 415051
-MD5 (emboss/PHYLIP-3.6b.tar.gz) = 6f2c10438d788acf4a1dff23441b2a2c
-SHA256 (emboss/PHYLIP-3.6b.tar.gz) = 32aba94d0be011ee304e974657db11544297c008e53341cd000a1f412eb874e2
-SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1136746
-MD5 (emboss/TOPO-1.0.0.tar.gz) = 7b3355570ba36f7daf57dcbc717215ce
-SHA256 (emboss/TOPO-1.0.0.tar.gz) = ff10378b4ecad69ddb374cd47a7d3c7fa5975d6695057f05ea264940258ebaa3
-SIZE (emboss/TOPO-1.0.0.tar.gz) = 351796
-MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 4332d7de49b27f257b58a90510223eb7
-SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = de66ddfdb72ccf7291be614c9a83fd8fc47363191cb2c045b372de5cc334a594
-SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 347672
-MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = c62f9b69a9ed9580d4489a8de9ea4863
-SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = f4933b62e19ee6b23a78b70c3cf2d5a9a18eff1d7532f92e2d33b1d683877916
-SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 352793
-MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 1e30e12048609a468b7b4d4affb177cf
-SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = c6bb252beaccac5256d99301933b15da6ef90af3f20d7f92fed1f78b271785ee
-SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 400125
-MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6efc35eb2855738252e0537198f5225d
-SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 7142e207987da46cd85c81088ea475abb866da90ff57e4c3ca1c63bd8f209b64
-SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 362563
-MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 15d5bc7b0ce9dfb113777c06c4e18906
-SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = 0a19ebbe52da849fb87799edaea2281a1bf235e6045725789b9b29e58f0a0dc5
-SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 323628
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0be3c59550e1e22924ea2540b11af275
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = b81fde3ab329ab75482b341568ef2965d99803765438f3825688a0d2abc05ca6
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420051
+MD5 (emboss/EMNU-1.05.tar.gz) = 64d8b9c2cd1a566aebb3355eb684bd35
+SHA256 (emboss/EMNU-1.05.tar.gz) = 56a55f336b0083ecfd2fd2dae0613f46e802eacb3214c16fc1966e6516795b95
+SIZE (emboss/EMNU-1.05.tar.gz) = 389665
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = ee65d0da0f2d75959f370b13f2218c1c
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = eee1cc8fef40e19fab74b16f1c1cb0883a49561eb9fdc2075f428085c6722bda
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431329
+MD5 (emboss/HMMER-2.3.2.tar.gz) = 3aa5707db81854f2674bf27aaeb1362e
+SHA256 (emboss/HMMER-2.3.2.tar.gz) = 31bbcca1f71b82170a65c4438f9cb9f1dfe3d4e066037a852060b010e3e39b5b
+SIZE (emboss/HMMER-2.3.2.tar.gz) = 565223
+MD5 (emboss/MEME-0.1.0.tar.gz) = d304f3b8a8e15af4dfa7b295655d80ec
+SHA256 (emboss/MEME-0.1.0.tar.gz) = ed4c02010af036515203661c28776b5e773e77eccad59990b7ac1410399d45ef
+SIZE (emboss/MEME-0.1.0.tar.gz) = 448413
+MD5 (emboss/MSE-1.0.0.tar.gz) = 3978a06e3651104f622a5834523c45de
+SHA256 (emboss/MSE-1.0.0.tar.gz) = e35560310ece8bb2dec7eeb88e99f39f313bf7366afc445e3b074b687e7f36b2
+SIZE (emboss/MSE-1.0.0.tar.gz) = 445013
+MD5 (emboss/PHYLIP-3.6b.tar.gz) = 760a90bea49872aba95fd7dd2b67570c
+SHA256 (emboss/PHYLIP-3.6b.tar.gz) = c2397937f4b827844192a33b31f13271a3560c81045543d912a9c28eb6ad894f
+SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1594433
+MD5 (emboss/TOPO-1.0.0.tar.gz) = d45602a1b1f22da50a775c41df5fe672
+SHA256 (emboss/TOPO-1.0.0.tar.gz) = ed1921e92d1bbd9fcc16ab36f2fcbafca9e60cc0d4b4fd1da77660ffd3e7b2f2
+SIZE (emboss/TOPO-1.0.0.tar.gz) = 379381
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = e5d004c1223116abaebb6657ae4a80fa
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = aa61cfc6da3cc478dd7f476537cdc6d966b00b90e2adedc709eb75e39e840c5c
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 460530
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = 778ab15bce09a6440fc6859b3a27157d
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = 23e069161ec56df5eab5fc491ca3493c056cfee42f2e05f1b5ef258498792a87
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 469776
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 26deae308cc5aac3dee5dd03df2ae9e8
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 9b0529befdbe5d56b3370cfffe0a4b4cc523f350b50ddd4a61dd24776a1770e8
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 573992
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6736b4741b15d4cba488a5422fcfaee1
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 3ed8ea5373232cd80302ff3b8727838b4de2f6b39aa263ab9530bbbe71d730c1
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 530874
+MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 9c3d6ea80166f62cd6ee63dfcb7e57a4
+SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = dc21b1772c2d76ed1c717eba6f8443b86cdf2e3cbcf71e056cdb9723138e4440
+SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 354179
+MD5 (emboss/VIENNA-1.6.tar.gz) = 282ed7ac9c1741160fcb1e8d48539311
+SHA256 (emboss/VIENNA-1.6.tar.gz) = 04c4a57486e23c2cc8ef396d9012c396519b2ab1b13b2500199e6457a34cfa58
+SIZE (emboss/VIENNA-1.6.tar.gz) = 635638
diff -ruN --exclude CVS /usr/ports/biology/embassy/pkg-plist embassy/pkg-plist
--- /usr/ports/biology/embassy/pkg-plist Fri Mar 31 06:43:21 2006
+++ embassy/pkg-plist Wed Apr 2 13:10:24 2008
@@ -1,201 +1,441 @@
-%%PLIST_DOMAINATRIX%%bin/cathparse
-%%PLIST_DOMAINATRIX%%bin/domainnr
-%%PLIST_DOMAINATRIX%%bin/domainreso
-%%PLIST_DOMAINATRIX%%bin/domainseqs
-%%PLIST_DOMAINATRIX%%bin/domainsse
-%%PLIST_DOMAINATRIX%%bin/scopparse
-%%PLIST_DOMAINATRIX%%bin/ssematch
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
-%%PLIST_DOMALIGN%%bin/allversusall
-%%PLIST_DOMALIGN%%bin/domainalign
-%%PLIST_DOMALIGN%%bin/domainrep
-%%PLIST_DOMALIGN%%bin/seqalign
-%%PLIST_DOMALIGN%%share/EMBOSS/acd/allversusall.acd
-%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd
-%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd
-%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd
-%%PLIST_DOMSEARCH%%bin/seqfraggle
-%%PLIST_DOMSEARCH%%bin/seqnr
-%%PLIST_DOMSEARCH%%bin/seqsearch
-%%PLIST_DOMSEARCH%%bin/seqsort
-%%PLIST_DOMSEARCH%%bin/seqwords
-%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
-%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd
-%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd
-%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
-%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
-%%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
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>Release-Note:
>Audit-Trail:
>Unformatted:
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