From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Apr 4 05:00:15 2008 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id DB8B31065671 for ; Fri, 4 Apr 2008 05:00:14 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id B065D8FC19 for ; Fri, 4 Apr 2008 05:00:14 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.2/8.14.2) with ESMTP id m3450CgE076764 for ; Fri, 4 Apr 2008 05:00:12 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.2/8.14.1/Submit) id m3450CYN076762; Fri, 4 Apr 2008 05:00:12 GMT (envelope-from gnats) Resent-Date: Fri, 4 Apr 2008 05:00:12 GMT Resent-Message-Id: <200804040500.m3450CYN076762@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Fernan Aguero Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id C6251106564A for ; Fri, 4 Apr 2008 04:54:00 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id ACC658FC12 for ; Fri, 4 Apr 2008 04:54:00 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.2/8.14.2) with ESMTP id m344rsGU099127 for ; Fri, 4 Apr 2008 04:53:54 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.2/8.14.1/Submit) id m344rssx099126; Fri, 4 Apr 2008 04:53:54 GMT (envelope-from nobody) Message-Id: <200804040453.m344rssx099126@www.freebsd.org> Date: Fri, 4 Apr 2008 04:53:54 GMT From: Fernan Aguero To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/122437: [maintainer] update emboss and embassy to v5.0.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 04 Apr 2008 05:00:15 -0000 >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 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-%%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 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+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordfinder.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/antigenic.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranambig.txt +%%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 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 # -# $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 @@ -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 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+%%PLIST_DOMALIGN%%emboss/share/EMBOSS/acd/domainalign.acd +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/acd/domainrep.acd +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/acd/seqalign.acd +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/html/embassy/domalign/index.html +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/html/embassy/domalign/allversusall.html +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/html/embassy/domalign/domainalign.html +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/html/embassy/domalign/domainrep.html +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/html/embassy/domalign/seqalign.html +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/programs/text/allversusall.txt +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/programs/text/domainalign.txt +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/programs/text/domainrep.txt +%%PLIST_DOMALIGN%%emboss/share/EMBOSS/doc/programs/text/seqalign.txt +%%PLIST_DOMSEARCH%%emboss/bin/seqnr +%%PLIST_DOMSEARCH%%emboss/bin/seqsearch +%%PLIST_DOMSEARCH%%emboss/bin/seqfraggle 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+%%PLIST_DOMSEARCH%%emboss/share/EMBOSS/doc/programs/text/seqsearch.txt +%%PLIST_DOMSEARCH%%emboss/share/EMBOSS/doc/programs/text/seqsort.txt +%%PLIST_DOMSEARCH%%emboss/share/EMBOSS/doc/programs/text/seqwords.txt +%%PLIST_EMNU%%emboss/bin/emnu +%%PLIST_EMNU%%emboss/share/EMBOSS/acd/emnu.acd +%%PLIST_EMNU%%emboss/share/EMBOSS/doc/html/embassy/emnu/index.html +%%PLIST_EMNU%%emboss/share/EMBOSS/doc/html/embassy/emnu/emnu.html +%%PLIST_EMNU%%emboss/share/EMBOSS/doc/programs/text/emnu.txt +%%PLIST_ESIM4%%emboss/bin/esim4 +%%PLIST_ESIM4%%emboss/share/EMBOSS/acd/esim4.acd +%%PLIST_ESIM4%%emboss/share/EMBOSS/doc/html/embassy/esim4/index.html +%%PLIST_ESIM4%%emboss/share/EMBOSS/doc/html/embassy/esim4/esim4.html +%%PLIST_ESIM4%%emboss/share/EMBOSS/doc/programs/text/esim4.txt +%%PLIST_HMMER%%emboss/bin/ehmmcalibrate +%%PLIST_HMMER%%emboss/bin/ehmmconvert +%%PLIST_HMMER%%emboss/bin/ehmmemit +%%PLIST_HMMER%%emboss/bin/ehmmfetch +%%PLIST_HMMER%%emboss/bin/ehmmindex 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