svn commit: r356575 - in head/biology/emboss: . files
Martin Wilke
miwi at FreeBSD.org
Thu Jun 5 03:28:08 UTC 2014
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= ${PORTNAME}
MAINTAINER= wen at FreeBSD.org
COMMENT= A collection of open source tools for genetic sequence analysis
+LICENSE= GPLv2
+
BUILD_DEPENDS= clustalw:${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
%%DATADIR%%/data/tp400_trans
-%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%DOCSDIR%%/manuals/admin.aux
-%%DOCSDIR%%/manuals/admin.dvi
-%%DOCSDIR%%/manuals/admin.log
-%%DOCSDIR%%/manuals/admin.pdf
-%%DOCSDIR%%/manuals/admin.ps
-%%DOCSDIR%%/manuals/admin.tex
-%%DOCSDIR%%/manuals/admin.toc
-%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%DOCSDIR%%/manuals/domainatrix.doc
-%%DOCSDIR%%/manuals/emboss.sty
-%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%DOCSDIR%%/manuals/emboss_qg.ps
-%%DOCSDIR%%/manuals/fdl.txt
-%%DOCSDIR%%/manuals/program.ps.gz
-%%DOCSDIR%%/programs/html/aaindexextract.html
-%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
-%%DOCSDIR%%/programs/html/abiview.html
-%%DOCSDIR%%/programs/html/acd_group.html
-%%DOCSDIR%%/programs/html/acdc.html
-%%DOCSDIR%%/programs/html/acdlog.html
-%%DOCSDIR%%/programs/html/acdpretty.html
-%%DOCSDIR%%/programs/html/acdtable.html
-%%DOCSDIR%%/programs/html/acdtrace.html
-%%DOCSDIR%%/programs/html/acdvalid.html
-%%DOCSDIR%%/programs/html/ajtest.html
-%%DOCSDIR%%/programs/html/aligncopy.html
-%%DOCSDIR%%/programs/html/aligncopypair.html
-%%DOCSDIR%%/programs/html/alignment_consensus_group.html
-%%DOCSDIR%%/programs/html/alignment_differences_group.html
-%%DOCSDIR%%/programs/html/alignment_dot_plots_group.html
-%%DOCSDIR%%/programs/html/alignment_global_group.html
-%%DOCSDIR%%/programs/html/alignment_local_group.html
-%%DOCSDIR%%/programs/html/alignment_multiple_group.html
-%%DOCSDIR%%/programs/html/antigenic.html
-%%DOCSDIR%%/programs/html/assembly_fragment_assembly_group.html
-%%DOCSDIR%%/programs/html/backtranambig.html
-%%DOCSDIR%%/programs/html/backtranseq.html
-%%DOCSDIR%%/programs/html/banana.1.banana.gif
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
More information about the svn-ports-all
mailing list