Date: Thu, 5 Jun 2014 03:28:07 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r356575 - in head/biology/emboss: . files Message-ID: <201406050328.s553S7Sn090077@svn.freebsd.org>
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Author: miwi Date: Thu Jun 5 03:28:06 2014 New Revision: 356575 URL: http://svnweb.freebsd.org/changeset/ports/356575 QAT: https://qat.redports.org/buildarchive/r356575/ Log: - Update to 6.6.0 - Stage support PR: 190508 Submitted by: Muhammad Moinur Rahman Added: head/biology/emboss/files/patch-Makefile.in (contents, props changed) head/biology/emboss/files/patch-emboss-Makefile.in (contents, props changed) Modified: head/biology/emboss/Makefile head/biology/emboss/distinfo head/biology/emboss/pkg-plist Modified: head/biology/emboss/Makefile ============================================================================== --- head/biology/emboss/Makefile Thu Jun 5 02:18:28 2014 (r356574) +++ head/biology/emboss/Makefile Thu Jun 5 03:28:06 2014 (r356575) @@ -2,17 +2,17 @@ # $FreeBSD$ PORTNAME= emboss -PORTVERSION= 6.2.0 -RELEASE= ${PORTNAME:tu}-${PORTVERSION} -PORTREVISION= 3 +PORTVERSION= 6.6.0 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ -DISTNAME= ${RELEASE} +DISTNAME= ${PORTNAME:tu}-${PORTVERSION} DIST_SUBDIR= ${PORTNAME} MAINTAINER= wen@FreeBSD.org COMMENT= A collection of open source tools for genetic sequence analysis +LICENSE= GPLv2 + BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \ primer3:${PORTSDIR}/biology/primer3 LIB_DEPENDS= libgd.so:${PORTSDIR}/graphics/gd \ @@ -22,37 +22,37 @@ CONFLICTS= qmail-ldap-[0-9]* digest-[0-9 PREFIX?= ${LOCALBASE}/emboss NO_MTREE= yes -USES= gmake +USES= gmake libtool iconv USE_SUBMAKE= yes GNU_CONFIGURE= yes -USE_AUTOTOOLS= libtool USE_LDCONFIG= yes SUB_FILES= pkg-message SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR} +LDFLAGS+= -L${LOCALBASE}/lib +CONFIGURE_ARGS+=${ICONV_CONFIGURE_ARG} DOCSDIR= ${PREFIX}/share/${PORTNAME:tu}/doc DATADIR= ${PREFIX}/share/${PORTNAME:tu} -CONFIGURE_ARGS+= --with-docroot=${DOCSDIR} - -.if !defined(WITHOUT_X11) -USE_XORG= x11 -USES+= motif -LIB_DEPENDS+= libgd.so:${PORTSDIR}/graphics/gd \ +OPTIONS_DEFINE= DOCS X11 +OPTIONS_DEFAULT= X11 +DOCS_CONFIGURE_ON= --with-docroot=${DOCSDIR} +X11_USE= XORG=x11 +X11_USES= motif +X11_LIB_DEPENDS= libgd.so:${PORTSDIR}/graphics/gd \ libpng15.so:${PORTSDIR}/graphics/png -.else -CONFIGURE_ARGS+= --without-x -.endif +X11_CONFIGURE_OFF= --without-x -DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template -NO_STAGE= yes +post-patch: + @${REINPLACE_CMD} -e 's/-liconv/${ICONV_LIB}/' ${WRKSRC}/configure + pre-install: - @ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE} + @ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${PREFIX}/share/${PORTNAME:tu}#' ${CONFIG_FILE} post-install: - ${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template - @ ${CAT} ${PKGMESSAGE} + ${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR} + ${CHOWN} ${SHAREOWN}:${SHAREGRP} ${STAGEDIR}${DATADIR}/emboss.default.template .include <bsd.port.mk> Modified: head/biology/emboss/distinfo ============================================================================== --- head/biology/emboss/distinfo Thu Jun 5 02:18:28 2014 (r356574) +++ head/biology/emboss/distinfo Thu Jun 5 03:28:06 2014 (r356575) @@ -1,2 +1,2 @@ -SHA256 (emboss/EMBOSS-6.2.0.tar.gz) = 4726371c0bcf3e232a5ee6b334e74b8c284dcbdcb176a475e77699515f8d122b -SIZE (emboss/EMBOSS-6.2.0.tar.gz) = 23430911 +SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e +SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028 Added: head/biology/emboss/files/patch-Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/emboss/files/patch-Makefile.in Thu Jun 5 03:28:06 2014 (r356575) @@ -0,0 +1,30 @@ +--- Makefile.in.orig 2014-05-29 03:27:28.070199330 +0600 ++++ Makefile.in 2014-05-29 03:28:00.167196553 +0600 +@@ -756,7 +756,7 @@ + + install-exec-am: + @$(NORMAL_INSTALL) +- $(MAKE) $(AM_MAKEFLAGS) install-exec-hook ++ $(MAKE) $(AM_MAKEFLAGS) + install-html: install-html-recursive + + install-html-am: +@@ -810,7 +810,7 @@ + distclean-libtool distclean-tags distcleancheck distdir \ + distuninstallcheck dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ +- install-dvi-am install-exec install-exec-am install-exec-hook \ ++ install-dvi-am install-exec install-exec-am \ + install-html install-html-am install-info install-info-am \ + install-man install-pdf install-pdf-am install-ps \ + install-ps-am install-strip installcheck installcheck-am \ +@@ -832,9 +832,6 @@ + tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + +-install-exec-hook: +- $(bindir)/embossupdate +- + # Tell versions [3.59,3.63) of GNU make to not export all variables. + # Otherwise a system limit (for SysV at least) may be exceeded. + .NOEXPORT: Added: head/biology/emboss/files/patch-emboss-Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/emboss/files/patch-emboss-Makefile.in Thu Jun 5 03:28:06 2014 (r356575) @@ -0,0 +1,10 @@ +--- emboss/Makefile.in.orig 2014-05-29 14:42:20.540406535 +0600 ++++ emboss/Makefile.in 2014-05-29 14:42:42.364404204 +0600 +@@ -3216,7 +3216,6 @@ + $(am__append_3) ../ajax/pcre/libepcre.la \ + ../plplot/libeplplot.la $(XLIB) + dist_pkgdata_DATA = \ +-emboss.default.template \ + emboss.standard \ + server.biomart \ + server.dasregistry \ Modified: head/biology/emboss/pkg-plist ============================================================================== --- head/biology/emboss/pkg-plist Thu Jun 5 02:18:28 2014 (r356574) +++ head/biology/emboss/pkg-plist Thu Jun 5 03:28:06 2014 (r356575) @@ -1,6 +1,8 @@ bin/aaindexextract bin/abiview bin/acdc +bin/acdgalaxy +bin/acdlog bin/acdpretty bin/acdtable bin/acdtrace @@ -8,11 +10,16 @@ bin/acdvalid bin/aligncopy bin/aligncopypair bin/antigenic +bin/assemblyget bin/backtranambig bin/backtranseq bin/banana bin/biosed bin/btwisted +bin/cachedas +bin/cachedbfetch +bin/cacheebeyesearch +bin/cacheensembl bin/cai bin/chaos bin/charge @@ -35,28 +42,50 @@ bin/dbiblast bin/dbifasta bin/dbiflat bin/dbigcg +bin/dbtell +bin/dbxcompress +bin/dbxedam bin/dbxfasta bin/dbxflat bin/dbxgcg +bin/dbxobo +bin/dbxreport +bin/dbxresource +bin/dbxstat +bin/dbxtax +bin/dbxuncompress bin/degapseq bin/density bin/descseq bin/diffseq -bin/digest bin/distmat bin/dotmatcher bin/dotpath bin/dottup bin/dreg +bin/drfinddata +bin/drfindformat +bin/drfindid +bin/drfindresource +bin/drget +bin/drtext +bin/edamdef +bin/edamhasinput +bin/edamhasoutput +bin/edamisformat +bin/edamisid +bin/edamname bin/edialign bin/einverted bin/embossdata +bin/embossupdate bin/embossversion bin/emma bin/emowse bin/entret bin/epestfind bin/eprimer3 +bin/eprimer32 bin/equicktandem bin/est2genome bin/etandem @@ -64,7 +93,9 @@ bin/extractalign bin/extractfeat bin/extractseq bin/featcopy +bin/featmerge bin/featreport +bin/feattext bin/findkm bin/freak bin/fuzznuc @@ -73,10 +104,13 @@ bin/fuzztran bin/garnier bin/geecee bin/getorf +bin/godef +bin/goname bin/helixturnhelix bin/hmoment bin/iep bin/infoalign +bin/infoassembly bin/infobase bin/inforesidue bin/infoseq @@ -113,11 +147,22 @@ bin/nthseq bin/nthseqset bin/octanol bin/oddcomp +bin/ontocount +bin/ontoget +bin/ontogetcommon +bin/ontogetdown +bin/ontogetobsolete +bin/ontogetroot +bin/ontogetsibs +bin/ontogetup +bin/ontoisobsolete +bin/ontotext bin/palindrome bin/pasteseq bin/patmatdb bin/patmatmotifs bin/pepcoil +bin/pepdigest bin/pepinfo bin/pepnet bin/pepstats @@ -141,21 +186,27 @@ bin/psiphi bin/rebaseextract bin/recoder bin/redata +bin/refseqget bin/remap bin/restover bin/restrict bin/revseq -bin/runJemboss.csh +bin/runJemboss.sh bin/seealso +bin/seqcount bin/seqmatchall bin/seqret bin/seqretsetall bin/seqretsplit +bin/seqxref +bin/seqxrefget +bin/servertell bin/showalign bin/showdb bin/showfeat bin/showorf bin/showpep +bin/showserver bin/showseq bin/shuffleseq bin/sigcleave @@ -171,7 +222,13 @@ bin/stretcher bin/stssearch bin/supermatcher bin/syco +bin/taxget +bin/taxgetdown +bin/taxgetrank +bin/taxgetspecies +bin/taxgetup bin/tcode +bin/textget bin/textsearch bin/tfextract bin/tfm @@ -184,6 +241,8 @@ bin/trimseq bin/trimspace bin/twofeat bin/union +bin/urlget +bin/variationget bin/vectorstrip bin/water bin/whichdb @@ -191,18 +250,34 @@ bin/wobble bin/wordcount bin/wordfinder bin/wordmatch +bin/wossdata +bin/wossinput bin/wossname +bin/wossoperation +bin/wossoutput +bin/wossparam +bin/wosstopic +bin/xmlget +bin/xmltext bin/yank include/ajacd.h include/ajalign.h include/ajarch.h include/ajarr.h +include/ajassem.h +include/ajassemdata.h +include/ajassemdb.h +include/ajassemread.h +include/ajassemwrite.h include/ajassert.h include/ajax.h +include/ajbamindex.h include/ajbase.h include/ajcall.h +include/ajcigar.h include/ajcod.h include/ajdan.h +include/ajdas.h include/ajdefine.h include/ajdmx.h include/ajdom.h @@ -210,48 +285,113 @@ include/ajdomain.h include/ajexcept.h include/ajfeat.h include/ajfeatdata.h +include/ajfeatdb.h +include/ajfeatread.h +include/ajfeatwrite.h include/ajfile.h include/ajfiledata.h include/ajfileio.h include/ajfmt.h +include/ajftp.h include/ajgraph.h include/ajgraphstruct.h include/ajhist.h +include/ajhttp.h include/ajindex.h include/ajjava.h +include/ajlib.h include/ajlist.h +include/ajmart.h include/ajmath.h include/ajmatrices.h include/ajmem.h include/ajmess.h include/ajnam.h include/ajnexus.h +include/ajobo.h +include/ajobodata.h +include/ajobodb.h +include/ajoboread.h +include/ajobowrite.h include/ajpat.h include/ajpdb.h include/ajpdbio.h include/ajphylo.h +include/ajquery.h +include/ajquerydata.h include/ajrange.h +include/ajrefseq.h +include/ajrefseqdata.h +include/ajrefseqdb.h +include/ajrefseqread.h +include/ajrefseqwrite.h include/ajreg.h include/ajreport.h +include/ajresource.h +include/ajresourcedata.h +include/ajresourcedb.h +include/ajresourceread.h +include/ajresourcewrite.h include/ajseq.h include/ajseqabi.h +include/ajseqbam.h include/ajseqdata.h include/ajseqdb.h include/ajseqread.h include/ajseqtype.h include/ajseqwrite.h +include/ajsoap.h include/ajsort.h include/ajsql.h include/ajstr.h include/ajsys.h include/ajtable.h +include/ajtagval.h +include/ajtax.h +include/ajtaxdata.h +include/ajtaxdb.h +include/ajtaxread.h +include/ajtaxwrite.h +include/ajtext.h +include/ajtextdata.h +include/ajtextdb.h +include/ajtextread.h +include/ajtextwrite.h include/ajtime.h include/ajtranslate.h include/ajtree.h +include/ajurl.h +include/ajurldata.h +include/ajurldb.h +include/ajurlread.h +include/ajurlwrite.h include/ajutil.h +include/ajvar.h +include/ajvarbcf.h +include/ajvardata.h +include/ajvardb.h +include/ajvarread.h +include/ajvarwrite.h include/ajvector.h -include/crc32.h -include/deflate.h +include/ajxml.h +include/ajxmldata.h +include/ajxmldb.h +include/ajxmlread.h +include/ajxmlwrite.h +include/eexpat/ascii.h +include/eexpat/asciitab.h +include/eexpat/expat.h +include/eexpat/expat_config.h +include/eexpat/expat_external.h +include/eexpat/expatemboss.h +include/eexpat/iasciitab.h +include/eexpat/internal.h +include/eexpat/latin1tab.h +include/eexpat/nametab.h +include/eexpat/utf8tab.h +include/eexpat/xmlrole.h +include/eexpat/xmltok.h +include/eexpat/xmltok_impl.h include/embaln.h include/embcom.h include/embcons.h @@ -278,6 +418,7 @@ include/embread.h include/embshow.h include/embsig.h include/embword.h +include/ensalign.h include/ensanalysis.h include/ensassemblyexception.h include/ensassembly.h @@ -297,10 +438,18 @@ include/ensexon.h include/ensexternaldatabase.h include/ensfeature.h include/ensgene.h +include/ensgvallele.h +include/ensgvattribute.h +include/ensgvbaseadaptor.h +include/ensgvdatabaseadaptor.h include/ensgvdata.h +include/ensgvgenotype.h include/ensgvindividual.h include/ensgvpopulation.h include/ensgvsample.h +include/ensgvsource.h +include/ensgvsynonym.h +include/ensgvvariation.h include/ensintron.h include/enskaryotype.h include/ensmapper.h @@ -308,24 +457,39 @@ include/ensmarker.h include/ensmetacoordinate.h include/ensmetainformation.h include/ensmiscellaneous.h +include/ensontology.h +include/ensoperon.h include/ensprediction.h include/ensprojectionsegment.h +include/ensprotein.h include/ensqcalignment.h +include/ensqcdasfeature.h include/ensqcdatabase.h include/ensqc.h include/ensqcsequence.h +include/ensqcsubmission.h +include/ensqcvariation.h include/ensregistry.h include/ensrepeat.h include/ensseqregion.h include/enssequence.h include/enssequenceedit.h +include/enssimple.h include/ensslice.h +include/enssoftware.h include/ensstorable.h include/enstable.h include/enstranslation.h include/enstranscript.h include/ensutility.h include/ensvariation.h +include/epcre/pcre.h +include/epcre/pcre_config.h +include/epcre/pcre_internal.h +include/epcre/pcre_printint.src +include/epcre/pcreemboss.h +include/epcre/pcreposix.h +include/epcre/ucp.h include/eplplot/disptab.h include/eplplot/drivers.h include/eplplot/metadefs.h @@ -344,85 +508,78 @@ include/eplplot/plstrm.h include/eplplot/plunicode-type1.h include/eplplot/plxwd.h include/eplplot/ps.h -include/expat.h -include/expat_external.h -include/expatemboss.h -include/inffast.h -include/inffixed.h -include/inflate.h -include/inftrees.h -include/pcre.h -include/pcre_config.h -include/pcreemboss.h -include/pcre_internal.h -include/pcre_printint.src -include/pcreposix.h -include/trees.h -include/ucp.h -include/zconf.h -include/zlibemboss.h -include/zlib.h -include/zutil.h -lib/libacd.so.6 -lib/libacd.so -lib/libacd.la +include/ezlib/crc32.h +include/ezlib/deflate.h +include/ezlib/gzguts.h +include/ezlib/inffast.h +include/ezlib/inffixed.h +include/ezlib/inflate.h +include/ezlib/inftrees.h +include/ezlib/trees.h +include/ezlib/zconf.h +include/ezlib/zlib.h +include/ezlib/zlibemboss.h +include/ezlib/zutil.h lib/libacd.a +lib/libacd.so +lib/libacd.so.6 +lib/libacd.so.6.0.5 lib/libajax.a -lib/libajax.la lib/libajax.so lib/libajax.so.6 +lib/libajax.so.6.0.5 lib/libajaxdb.a -lib/libajaxdb.la lib/libajaxdb.so lib/libajaxdb.so.6 +lib/libajaxdb.so.6.0.5 lib/libajaxg.a -lib/libajaxg.la lib/libajaxg.so lib/libajaxg.so.6 +lib/libajaxg.so.6.0.5 lib/libeexpat.a -lib/libeexpat.la lib/libeexpat.so -lib/libeexpat.so.2 +lib/libeexpat.so.1 +lib/libeexpat.so.1.1.0 lib/libensembl.a -lib/libensembl.la lib/libensembl.so lib/libensembl.so.6 +lib/libensembl.so.6.0.5 lib/libepcre.a -lib/libepcre.la lib/libepcre.so lib/libepcre.so.7 +lib/libepcre.so.7.0.9 lib/libeplplot.a -lib/libeplplot.la lib/libeplplot.so -lib/libeplplot.so.5 +lib/libeplplot.so.3 +lib/libeplplot.so.3.2.7 lib/libezlib.a -lib/libezlib.la lib/libezlib.so -lib/libezlib.so.2 +lib/libezlib.so.1 +lib/libezlib.so.1.1.0 lib/libnucleus.a -lib/libnucleus.la lib/libnucleus.so lib/libnucleus.so.6 +lib/libnucleus.so.6.0.5 %%DATADIR%%/acd/aaindexextract.acd %%DATADIR%%/acd/abiview.acd %%DATADIR%%/acd/acdc.acd -%%DATADIR%%/acd/acdlog.acd %%DATADIR%%/acd/acdpretty.acd -%%DATADIR%%/acd/acdrelations.acd %%DATADIR%%/acd/acdtable.acd %%DATADIR%%/acd/acdtrace.acd %%DATADIR%%/acd/acdvalid.acd -%%DATADIR%%/acd/ajbad.acd -%%DATADIR%%/acd/ajfeatest.acd -%%DATADIR%%/acd/ajtest.acd %%DATADIR%%/acd/aligncopy.acd %%DATADIR%%/acd/aligncopypair.acd %%DATADIR%%/acd/antigenic.acd +%%DATADIR%%/acd/assemblyget.acd %%DATADIR%%/acd/backtranambig.acd %%DATADIR%%/acd/backtranseq.acd %%DATADIR%%/acd/banana.acd %%DATADIR%%/acd/biosed.acd %%DATADIR%%/acd/btwisted.acd +%%DATADIR%%/acd/cachedas.acd +%%DATADIR%%/acd/cachedbfetch.acd +%%DATADIR%%/acd/cacheebeyesearch.acd +%%DATADIR%%/acd/cacheensembl.acd %%DATADIR%%/acd/cai.acd %%DATADIR%%/acd/chaos.acd %%DATADIR%%/acd/charge.acd @@ -433,11 +590,9 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/codcopy.acd %%DATADIR%%/acd/coderet.acd %%DATADIR%%/acd/codes.english -%%DATADIR%%/acd/complex.acd %%DATADIR%%/acd/compseq.acd %%DATADIR%%/acd/cons.acd %%DATADIR%%/acd/consambig.acd -%%DATADIR%%/acd/corbatest.acd %%DATADIR%%/acd/cpgplot.acd %%DATADIR%%/acd/cpgreport.acd %%DATADIR%%/acd/cusp.acd @@ -448,11 +603,18 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/dbifasta.acd %%DATADIR%%/acd/dbiflat.acd %%DATADIR%%/acd/dbigcg.acd +%%DATADIR%%/acd/dbtell.acd +%%DATADIR%%/acd/dbxcompress.acd +%%DATADIR%%/acd/dbxedam.acd %%DATADIR%%/acd/dbxfasta.acd %%DATADIR%%/acd/dbxflat.acd %%DATADIR%%/acd/dbxgcg.acd +%%DATADIR%%/acd/dbxobo.acd %%DATADIR%%/acd/dbxreport.acd +%%DATADIR%%/acd/dbxresource.acd %%DATADIR%%/acd/dbxstat.acd +%%DATADIR%%/acd/dbxtax.acd +%%DATADIR%%/acd/dbxuncompress.acd %%DATADIR%%/acd/degapseq.acd %%DATADIR%%/acd/density.acd %%DATADIR%%/acd/descseq.acd @@ -463,18 +625,29 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/dotpath.acd %%DATADIR%%/acd/dottup.acd %%DATADIR%%/acd/dreg.acd -%%DATADIR%%/acd/edamclean.acd +%%DATADIR%%/acd/drfinddata.acd +%%DATADIR%%/acd/drfindformat.acd +%%DATADIR%%/acd/drfindid.acd +%%DATADIR%%/acd/drfindresource.acd +%%DATADIR%%/acd/drget.acd +%%DATADIR%%/acd/drtext.acd +%%DATADIR%%/acd/edamdef.acd +%%DATADIR%%/acd/edamhasinput.acd +%%DATADIR%%/acd/edamhasoutput.acd +%%DATADIR%%/acd/edamisformat.acd +%%DATADIR%%/acd/edamisid.acd +%%DATADIR%%/acd/edamname.acd %%DATADIR%%/acd/edialign.acd %%DATADIR%%/acd/einverted.acd %%DATADIR%%/acd/embossdata.acd %%DATADIR%%/acd/embossversion.acd +%%DATADIR%%/acd/embossupdate.acd %%DATADIR%%/acd/emma.acd %%DATADIR%%/acd/emowse.acd -%%DATADIR%%/acd/ensembltest.acd -%%DATADIR%%/acd/entrails.acd %%DATADIR%%/acd/entret.acd %%DATADIR%%/acd/epestfind.acd %%DATADIR%%/acd/eprimer3.acd +%%DATADIR%%/acd/eprimer32.acd %%DATADIR%%/acd/equicktandem.acd %%DATADIR%%/acd/est2genome.acd %%DATADIR%%/acd/etandem.acd @@ -482,7 +655,9 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/extractfeat.acd %%DATADIR%%/acd/extractseq.acd %%DATADIR%%/acd/featcopy.acd +%%DATADIR%%/acd/featmerge.acd %%DATADIR%%/acd/featreport.acd +%%DATADIR%%/acd/feattext.acd %%DATADIR%%/acd/findkm.acd %%DATADIR%%/acd/freak.acd %%DATADIR%%/acd/fuzznuc.acd @@ -491,16 +666,17 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/garnier.acd %%DATADIR%%/acd/geecee.acd %%DATADIR%%/acd/getorf.acd +%%DATADIR%%/acd/godef.acd +%%DATADIR%%/acd/goname.acd %%DATADIR%%/acd/groups.standard %%DATADIR%%/acd/helixturnhelix.acd -%%DATADIR%%/acd/histogramtest.acd %%DATADIR%%/acd/hmoment.acd %%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/infoalign.acd +%%DATADIR%%/acd/infoassembly.acd %%DATADIR%%/acd/infobase.acd %%DATADIR%%/acd/inforesidue.acd %%DATADIR%%/acd/infoseq.acd -%%DATADIR%%/acd/intconv.acd %%DATADIR%%/acd/isochore.acd %%DATADIR%%/acd/jaspextract.acd %%DATADIR%%/acd/jaspscan.acd @@ -523,7 +699,6 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/mwfilter.acd %%DATADIR%%/acd/needle.acd %%DATADIR%%/acd/needleall.acd -%%DATADIR%%/acd/newcoils.acd %%DATADIR%%/acd/newcpgreport.acd %%DATADIR%%/acd/newcpgseek.acd %%DATADIR%%/acd/newseq.acd @@ -536,14 +711,22 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/nthseqset.acd %%DATADIR%%/acd/octanol.acd %%DATADIR%%/acd/oddcomp.acd -%%DATADIR%%/acd/origsplitter.acd -%%DATADIR%%/acd/origunion.acd +%%DATADIR%%/acd/ontocount.acd +%%DATADIR%%/acd/ontoget.acd +%%DATADIR%%/acd/ontogetcommon.acd +%%DATADIR%%/acd/ontogetdown.acd +%%DATADIR%%/acd/ontogetobsolete.acd +%%DATADIR%%/acd/ontogetroot.acd +%%DATADIR%%/acd/ontogetsibs.acd +%%DATADIR%%/acd/ontogetup.acd +%%DATADIR%%/acd/ontoisobsolete.acd +%%DATADIR%%/acd/ontotext.acd %%DATADIR%%/acd/palindrome.acd %%DATADIR%%/acd/pasteseq.acd %%DATADIR%%/acd/patmatdb.acd %%DATADIR%%/acd/patmatmotifs.acd -%%DATADIR%%/acd/patmattest.acd %%DATADIR%%/acd/pepcoil.acd +%%DATADIR%%/acd/pepdigest.acd %%DATADIR%%/acd/pepinfo.acd %%DATADIR%%/acd/pepnet.acd %%DATADIR%%/acd/pepstats.acd @@ -556,8 +739,6 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/preg.acd %%DATADIR%%/acd/prettyplot.acd %%DATADIR%%/acd/prettyseq.acd -%%DATADIR%%/acd/prima.acd -%%DATADIR%%/acd/primers.acd %%DATADIR%%/acd/primersearch.acd %%DATADIR%%/acd/printsextract.acd %%DATADIR%%/acd/profit.acd @@ -569,28 +750,28 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/rebaseextract.acd %%DATADIR%%/acd/recoder.acd %%DATADIR%%/acd/redata.acd +%%DATADIR%%/acd/refseqget.acd %%DATADIR%%/acd/remap.acd %%DATADIR%%/acd/restover.acd %%DATADIR%%/acd/restrict.acd %%DATADIR%%/acd/revseq.acd %%DATADIR%%/acd/sections.standard %%DATADIR%%/acd/seealso.acd -%%DATADIR%%/acd/seqinfo.acd +%%DATADIR%%/acd/seqcount.acd %%DATADIR%%/acd/seqmatchall.acd %%DATADIR%%/acd/seqret.acd -%%DATADIR%%/acd/seqretall.acd -%%DATADIR%%/acd/seqretallfeat.acd -%%DATADIR%%/acd/seqretset.acd %%DATADIR%%/acd/seqretsetall.acd -%%DATADIR%%/acd/seqretsingle.acd %%DATADIR%%/acd/seqretsplit.acd -%%DATADIR%%/acd/seqrettype.acd +%%DATADIR%%/acd/seqxref.acd +%%DATADIR%%/acd/seqxrefget.acd +%%DATADIR%%/acd/servertell.acd %%DATADIR%%/acd/showalign.acd %%DATADIR%%/acd/showdb.acd %%DATADIR%%/acd/showfeat.acd %%DATADIR%%/acd/showorf.acd %%DATADIR%%/acd/showpep.acd %%DATADIR%%/acd/showseq.acd +%%DATADIR%%/acd/showserver.acd %%DATADIR%%/acd/shuffleseq.acd %%DATADIR%%/acd/sigcleave.acd %%DATADIR%%/acd/silent.acd @@ -601,13 +782,17 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/skipseq.acd %%DATADIR%%/acd/splitsource.acd %%DATADIR%%/acd/splitter.acd -%%DATADIR%%/acd/sqltest.acd %%DATADIR%%/acd/stretcher.acd %%DATADIR%%/acd/stssearch.acd %%DATADIR%%/acd/supermatcher.acd %%DATADIR%%/acd/syco.acd +%%DATADIR%%/acd/taxget.acd +%%DATADIR%%/acd/taxgetdown.acd +%%DATADIR%%/acd/taxgetrank.acd +%%DATADIR%%/acd/taxgetspecies.acd +%%DATADIR%%/acd/taxgetup.acd %%DATADIR%%/acd/tcode.acd -%%DATADIR%%/acd/testplot.acd +%%DATADIR%%/acd/textget.acd %%DATADIR%%/acd/textsearch.acd %%DATADIR%%/acd/tfextract.acd %%DATADIR%%/acd/tfm.acd @@ -615,13 +800,14 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/tmap.acd %%DATADIR%%/acd/tranalign.acd %%DATADIR%%/acd/transeq.acd -%%DATADIR%%/acd/treetypedisplay.acd %%DATADIR%%/acd/trimest.acd %%DATADIR%%/acd/trimseq.acd %%DATADIR%%/acd/trimspace.acd %%DATADIR%%/acd/twofeat.acd %%DATADIR%%/acd/union.acd +%%DATADIR%%/acd/urlget.acd %%DATADIR%%/acd/variables.standard +%%DATADIR%%/acd/variationget.acd %%DATADIR%%/acd/vectorstrip.acd %%DATADIR%%/acd/water.acd %%DATADIR%%/acd/whichdb.acd @@ -629,7 +815,15 @@ lib/libnucleus.so.6 %%DATADIR%%/acd/wordcount.acd %%DATADIR%%/acd/wordfinder.acd %%DATADIR%%/acd/wordmatch.acd +%%DATADIR%%/acd/wossdata.acd +%%DATADIR%%/acd/wossinput.acd %%DATADIR%%/acd/wossname.acd +%%DATADIR%%/acd/wossoperation.acd +%%DATADIR%%/acd/wossoutput.acd +%%DATADIR%%/acd/wossparam.acd +%%DATADIR%%/acd/wosstopic.acd +%%DATADIR%%/acd/xmlget.acd +%%DATADIR%%/acd/xmltext.acd %%DATADIR%%/acd/yank.acd %%DATADIR%%/data/AAINDEX/dummyfile %%DATADIR%%/data/CODONS/Cut.index @@ -882,6 +1076,7 @@ lib/libnucleus.so.6 %%DATADIR%%/data/CODONS/Eysp.cut %%DATADIR%%/data/CODONS/Ezebrafish.cut %%DATADIR%%/data/CODONS/Ezma.cut +%%DATADIR%%/data/DRCAT.dat %%DATADIR%%/data/EBLOSUM30 %%DATADIR%%/data/EBLOSUM35 %%DATADIR%%/data/EBLOSUM40 @@ -898,8 +1093,10 @@ lib/libnucleus.so.6 %%DATADIR%%/data/EBLOSUM85 %%DATADIR%%/data/EBLOSUM90 %%DATADIR%%/data/EBLOSUMN +%%DATADIR%%/data/EDAM.obo %%DATADIR%%/data/EDNAFULL %%DATADIR%%/data/EDNAMAT +%%DATADIR%%/data/EDNASIMPLE %%DATADIR%%/data/EGC.0 %%DATADIR%%/data/EGC.1 %%DATADIR%%/data/EGC.10 @@ -986,10 +1183,10 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Eenergy.dat %%DATADIR%%/data/Efeatures.embl %%DATADIR%%/data/Efeatures.emboss -%%DATADIR%%/data/Efeatures.gff +%%DATADIR%%/data/Efeatures.gff2 +%%DATADIR%%/data/Efeatures.gff2protein %%DATADIR%%/data/Efeatures.gff3 %%DATADIR%%/data/Efeatures.gff3protein -%%DATADIR%%/data/Efeatures.gffprotein %%DATADIR%%/data/Efeatures.pir %%DATADIR%%/data/Efeatures.refseqp %%DATADIR%%/data/Efeatures.protein @@ -1007,9 +1204,9 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Enakai.dat %%DATADIR%%/data/EnsemblAliases.dat %%DATADIR%%/data/EnsemblIdentifiers.dat -%%DATADIR%%/data/Etags.gff3protein %%DATADIR%%/data/Epepcoil.dat %%DATADIR%%/data/Epk.dat +%%DATADIR%%/data/Epkexpasy.dat %%DATADIR%%/data/Epprofile %%DATADIR%%/data/Eprior1.plib %%DATADIR%%/data/Eprior30.plib @@ -1019,9 +1216,10 @@ lib/libnucleus.so.6 %%DATADIR%%/data/Esig.pro %%DATADIR%%/data/Etags.embl %%DATADIR%%/data/Etags.emboss -%%DATADIR%%/data/Etags.gff +%%DATADIR%%/data/Etags.gff2 +%%DATADIR%%/data/Etags.gff2protein %%DATADIR%%/data/Etags.gff3 -%%DATADIR%%/data/Etags.gffprotein +%%DATADIR%%/data/Etags.gff3protein %%DATADIR%%/data/Etags.pir %%DATADIR%%/data/Etags.protein %%DATADIR%%/data/Etags.refseqp @@ -1032,589 +1230,193 @@ lib/libnucleus.so.6 %%DATADIR%%/data/JASPAR_CNE/dummyfile %%DATADIR%%/data/JASPAR_CORE/dummyfile %%DATADIR%%/data/JASPAR_FAM/dummyfile +%%DATADIR%%/data/JASPAR_PBM/dummyfile +%%DATADIR%%/data/JASPAR_PBM_HLH/dummyfile +%%DATADIR%%/data/JASPAR_PBM_HOMEO/dummyfile %%DATADIR%%/data/JASPAR_PHYLOFACTS/dummyfile %%DATADIR%%/data/JASPAR_POLII/dummyfile %%DATADIR%%/data/JASPAR_SPLICE/dummyfile %%DATADIR%%/data/Matrices.nucleotide %%DATADIR%%/data/Matrices.protein %%DATADIR%%/data/Matrices.proteinstructure +%%DATADIR%%/data/OBO/chebi.obo +%%DATADIR%%/data/OBO/eco.obo +%%DATADIR%%/data/OBO/go.obo +%%DATADIR%%/data/OBO/pathway.obo +%%DATADIR%%/data/OBO/ro.obo +%%DATADIR%%/data/OBO/so.obo +%%DATADIR%%/data/OBO/software.obo %%DATADIR%%/data/PRINTS/dummyfile %%DATADIR%%/data/PROSITE/dummyfile -%%DATADIR%%/data/REBASE/dummyfile +%%DATADIR%%/data/REBASE/embossre.equ %%DATADIR%%/data/SSSUB +%%DATADIR%%/data/TAXONOMY/division.dmp +%%DATADIR%%/data/TAXONOMY/gencode.dmp +%%DATADIR%%/data/TAXONOMY/merged.dmp +%%DATADIR%%/data/TAXONOMY/names.dmp +%%DATADIR%%/data/TAXONOMY/nodes.dmp %%DATADIR%%/data/edialignmat -%%DATADIR%%/data/embossre.equ %%DATADIR%%/data/tp400_dna %%DATADIR%%/data/tp400_prot 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