FreeBSD Bugzilla – Attachment 48577 Details for
Bug 74333
update biology/emboss and take maintainership
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[patch]
emboss.diff
emboss.diff (text/plain), 112.92 KB, created by
Fernan Aguero
on 2004-11-24 20:00:46 UTC
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Description:
emboss.diff
Filename:
MIME Type:
Creator:
Fernan Aguero
Created:
2004-11-24 20:00:46 UTC
Size:
112.92 KB
patch
obsolete
>diff -ruN /usr/ports/biology/emboss/Makefile emboss/Makefile >--- /usr/ports/biology/emboss/Makefile Mon Nov 22 06:09:09 2004 >+++ emboss/Makefile Wed Nov 24 16:04:45 2004 >@@ -2,141 +2,56 @@ > # Date created: 31 July 2000 > # Whom: Johann Visagie <johann@egenetics.com> > # >-# $FreeBSD: ports/biology/emboss/Makefile,v 1.40 2004/11/20 07:40:43 linimon Exp $ >+# $FreeBSD: ports/biology/emboss/Makefile,v 1.39 2004/06/23 08:20:21 vs Exp $ > # > > PORTNAME= emboss >-PORTVERSION= 2.4.1 >-PORTREVISION= 3 >+PORTVERSION= 2.9.0 > CATEGORIES= biology >-MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/old/ \ >- ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/ >-# ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ >+MASTER_SITES= 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} >-DIST_SUBDIR= ${PORTNAME} >-EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} > >-MAINTAINER= ports@FreeBSD.org >+MAINTAINER= fernan@iib.unsam.edu.ar > COMMENT= A collection of open source tools for genetic sequence analysis > >-LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd >+BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \ >+ primer3:${PORTSDIR}/biology/primer3 >+LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \ >+ png.5:${PORTSDIR}/graphics/png > > USE_SUBMAKE= yes > USE_GMAKE= yes > GNU_CONFIGURE= yes >+USE_LIBTOOL_VER=15 > INSTALLS_SHLIB= yes > USE_XLIB= yes > USE_MOTIF= yes >-USE_PERL5_BUILD=yes >+USE_REINPLACE= yes > PKGMESSAGE= ${WRKDIR}/pkg-message > >-.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc) >-.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc" >-.endif >- >-CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include" \ >- LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib" >-SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ >- MKDIR="${MKDIR}" RM="${RM}" >- >-WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} >-EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY >-EMNU_VERSION= 1.0.5 >-HMMER_VERSION= 2.1.1 >-MEME_VERSION= 2.3.1 >-MSE_VERSION= 0.0.4 >-TOPO_VERSION= 0.1 >-PHYLIP_VERSION= 3.573c > DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html > CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template > >-.for app in EMNU HMMER MEME MSE PHYLIP TOPO >-SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" >-.if defined(WITH_${app}) >-APPLIST+= ${app} >-${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} >-${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} >-DISTFILES+= ${${app}_DISTFILE} >-PLIST_${app}= "" >-.else >-PLIST_${app}= "@comment " >-.endif >-PLIST_SUB+= PLIST_${app}=${PLIST_${app}} >-.endfor >- >-# Jemboss support is a work in progress. >-# >-#.if defined(WITH_JEMBOSS) >-#USE_JAVA= 1.3+ >-#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \ >-# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L} >-#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin >-#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin >-#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss >-#.endif >- >-pre-fetch: >- @ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME} >- >-post-extract: >-.for app in ${APPLIST} >- @ ${MKDIR} ${EMBASSY_WRKDIR} >- @ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \ >- ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS} >- @ if [ `id -u` = 0 ]; then \ >- ${CHMOD} -R ug-s ${${app}_WRKSRC}; \ >- ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ >- fi >-.endfor >- > post-patch: >+.if !defined(NOPORTDOCS) > .for DIR in ${DOC_DIRS} >- @ ${PERL} -pi.orig -e \ >- 's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \ >+ ${REINPLACE_CMD} -e \ >+ 's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \ > ${WRKSRC}/${DIR}/Makefile.in > .endfor >- >-post-configure: >-.for app in ${APPLIST} >- @ cd ${${app}_WRKSRC} && \ >- ${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \ >- CXXFLAGS="${CXXFLAGS}" \ >- INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \ >- INSTALL_DATA="${INSTALL_DATA}" \ >- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ >- INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ >- ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} >-.endfor >- >-post-build: >-.for app in ${APPLIST} >- @ cd ${${app}_WRKSRC} && \ >- ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ >- ${MAKE_ARGS} >-.endfor >-#.if defined(WITH_JEMBOSS) >-# @ cd ${JEMBOSS_WRKSRC} && \ >-# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ >-# ${MAKE_ARGS} >-#.endif >+.endif > > post-install: >-.for app in ${APPLIST} >- @ cd ${${app}_WRKSRC} && \ >- ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ >- ${MAKE_ARGS} ${INSTALL_TARGET} >-.endfor >- @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ >- ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ >- ${CHOWN} ${SHAREOWN}:${SHAREGRP} \ >- ${PREFIX}/etc/emboss.default.sample >- @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ >- pkg-message > ${PKGMESSAGE} >+ @ cd ${WRKSRC} && \ >+ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' \ >+ ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ >+ ${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample >+ @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE} > .if !defined(BATCH) > @ ${CAT} ${PKGMESSAGE} > .endif >- >-post-clean: >- @ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc > > .include <bsd.port.mk> >diff -ruN /usr/ports/biology/emboss/distinfo emboss/distinfo >--- /usr/ports/biology/emboss/distinfo Mon Sep 30 16:23:36 2002 >+++ emboss/distinfo Thu Nov 4 17:15:33 2004 >@@ -1,7 +1,2 @@ >-MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad >-MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66 >-MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21 >-MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c >-MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9 >-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084 >-MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a >+MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472 >+SIZE (EMBOSS-2.9.0.tar.gz) = 14479274 >diff -ruN /usr/ports/biology/emboss/files/patch-aa emboss/files/patch-aa >--- /usr/ports/biology/emboss/files/patch-aa Wed Jul 11 10:33:34 2001 >+++ emboss/files/patch-aa Wed Dec 31 21:00:00 1969 >@@ -1,26 +0,0 @@ >-Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still >-waiting for this to be incorporated into an official release of EMBOSS.) >- >-The port installs ${PREFIX}/etc/emboss.default.sample >- >--- Johann <wjv@FreeBSD.org> >- >- >---- ajax/ajnam.c.orig Thu Aug 17 20:31:30 2000 >-+++ ajax/ajnam.c Mon Aug 28 15:12:09 2000 >-@@ -984,6 +984,15 @@ >- prefixRootFile = fopen (ajStrStr(namRootStr), "r"); >- } >- >-+ /* look for $(PREFIX)_ROOT/../emboss.default */ >-+ >-+ if (!prefixRootFile) >-+ { >-+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", >-+ namInstallRoot, prefix); >-+ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); >-+ } >-+ >- if (namFileOrig) >- (void) ajStrAppC (&namFileOrig, ", "); >- (void) ajStrApp (&namFileOrig, namRootStr); >diff -ruN /usr/ports/biology/emboss/files/patch-ajax::ajjava.c emboss/files/patch-ajax::ajjava.c >--- /usr/ports/biology/emboss/files/patch-ajax::ajjava.c Fri Jul 5 07:09:32 2002 >+++ emboss/files/patch-ajax::ajjava.c Wed Dec 31 21:00:00 1969 >@@ -1,11 +0,0 @@ >---- ajax/ajjava.c.orig Thu May 2 22:06:08 2002 >-+++ ajax/ajjava.c Sun May 26 09:14:20 2002 >-@@ -75,7 +75,7 @@ >- #endif >- >- #ifndef __ppc__ >--#include <crypt.h> >-+#include <unistd.h> >- #endif >- >- >diff -ruN /usr/ports/biology/emboss/files/patch-configure emboss/files/patch-configure >--- /usr/ports/biology/emboss/files/patch-configure Mon Jan 29 12:48:01 2001 >+++ emboss/files/patch-configure Wed Dec 31 21:00:00 1969 >@@ -1,11 +0,0 @@ >---- configure.orig Mon Jan 22 23:28:17 2001 >-+++ configure Thu Jan 25 19:07:33 2001 >-@@ -1473,7 +1473,7 @@ >- >- >- >--AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" >-+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\"" >- >- #AC_PROG_CXX >- for ac_prog in mawk gawk nawk awk >diff -ruN /usr/ports/biology/emboss/files/patch-emboss-emboss.default.template emboss/files/patch-emboss-emboss.default.template >--- /usr/ports/biology/emboss/files/patch-emboss-emboss.default.template Wed May 30 11:34:56 2001 >+++ emboss/files/patch-emboss-emboss.default.template Wed Dec 31 21:00:00 1969 >@@ -1,38 +0,0 @@ >---- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001 >-+++ emboss/emboss.default.template Wed May 30 10:23:48 2001 >-@@ -1,9 +1,31 @@ >--#SET emboss_tempdata name_of_emboss_test_database_directory >-+##################################################### >-+### Configuration options for FreeBSD EMBOSS port ### >-+##################################################### >- >--# Logfile - set this to a file that any user can append to >--# and EMBOSS applications will automatically write log information >-+# The directory where EMBOSS expects to find run-time >-+# databases. This is the compiled-in default - change >-+# only if you know what you're doing! >-+# >-+#SET emboss_data %%PREFIX%%/share/EMBOSS/data >- >--#SET emboss_logfile /packages/emboss/emboss/log >-+# This is an alias which is internal to this >-+# configuration file and is set here merely as a >-+# convenience. It points to the location where you >-+# have placed your local databases (this will differ >-+# from site to site). >-+# >-+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases >-+ >-+# Logfile. If this is uncommented and set to a file >-+# that any user can append to, EMBOSS applications >-+# will automatically log usage information. >-+# >-+#SET emboss_logfile /var/log/emboss.log >-+ >-+ >-+########################################### >-+### Configuration options for databases ### >-+########################################### >- >- # swissprot (Puffer fish entries) >- # ========= >diff -ruN /usr/ports/biology/emboss/pkg-message emboss/pkg-message >--- /usr/ports/biology/emboss/pkg-message Wed Jul 11 10:58:12 2001 >+++ emboss/pkg-message Wed Nov 3 18:29:55 2004 >@@ -15,7 +15,8 @@ > system-wide emboss.default. > > Online EMBOSS documentation is available at: >- http://www.uk.embnet.org/Software/EMBOSS/general.html >+ http://www.uk.embnet.org/Software/EMBOSS/userdoc.html > http://www.uk.embnet.org/Software/EMBOSS/Doc/ >+ http://emboss.sourceforge.net/docs/ > > -------------------------------------------------------------------------- >diff -ruN /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist >--- /usr/ports/biology/emboss/pkg-plist Mon Sep 30 16:23:36 2002 >+++ emboss/pkg-plist Wed Nov 24 16:24:36 2004 >@@ -1,94 +1,10 @@ >-%%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 >-%%PLIST_MEME%%lib/libmeme.so.2 >-%%PLIST_MEME%%share/EMBOSS/acd/meme.acd >-%%PLIST_MSE%%bin/mse >-%%PLIST_MSE%%lib/libckit.a >-%%PLIST_MSE%%lib/libckit.la >-%%PLIST_MSE%%lib/libckit.so >-%%PLIST_MSE%%lib/libckit.so.1 >-%%PLIST_MSE%%share/EMBOSS/acd/mse.acd >-%%PLIST_PHYLIP%%bin/eclique >-%%PLIST_PHYLIP%%bin/econsense >-%%PLIST_PHYLIP%%bin/econtml >-%%PLIST_PHYLIP%%bin/econtrast >-%%PLIST_PHYLIP%%bin/ednacomp >-%%PLIST_PHYLIP%%bin/ednadist >-%%PLIST_PHYLIP%%bin/ednainvar >-%%PLIST_PHYLIP%%bin/ednaml >-%%PLIST_PHYLIP%%bin/ednamlk >-%%PLIST_PHYLIP%%bin/ednapars >-%%PLIST_PHYLIP%%bin/ednapenny >-%%PLIST_PHYLIP%%bin/edollop >-%%PLIST_PHYLIP%%bin/edolpenny >-%%PLIST_PHYLIP%%bin/efactor >-%%PLIST_PHYLIP%%bin/efitch >-%%PLIST_PHYLIP%%bin/egendist >-%%PLIST_PHYLIP%%bin/ekitsch >-%%PLIST_PHYLIP%%bin/emix >-%%PLIST_PHYLIP%%bin/eneighbor >-%%PLIST_PHYLIP%%bin/epenny >-%%PLIST_PHYLIP%%bin/eprotdist >-%%PLIST_PHYLIP%%bin/eprotpars >-%%PLIST_PHYLIP%%bin/erestml >-%%PLIST_PHYLIP%%bin/eseqboot >-%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd >-%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd >-%%PLIST_TOPO%%bin/topo >-%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd >+bin/aaindexextract > bin/abiview > bin/acdc >-bin/alignwrap >+bin/acdpretty >+bin/acdtable >+bin/acdtrace >+bin/acdvalid > bin/antigenic > bin/backtranseq > bin/banana >@@ -104,7 +20,6 @@ > bin/coderet > bin/compseq > bin/cons >-bin/contacts > bin/cpgplot > bin/cpgreport > bin/cusp >@@ -117,11 +32,9 @@ > bin/dbigcg > bin/degapseq > bin/descseq >-bin/dichet > bin/diffseq > bin/digest > bin/distmat >-bin/domainer > bin/dotmatcher > bin/dotpath > bin/dottup >@@ -132,6 +45,8 @@ > bin/emma > bin/emowse > bin/entret >+bin/epestfind >+bin/eprimer3 > bin/equicktandem > bin/est2genome > bin/etandem >@@ -151,6 +66,7 @@ > bin/infoalign > bin/infoseq > bin/isochore >+bin/jembossctl > bin/lindna > bin/listor > bin/marscan >@@ -160,14 +76,14 @@ > bin/megamerger > bin/merger > bin/msbar >+bin/mwcontam > bin/mwfilter > bin/needle > bin/newcpgreport > bin/newcpgseek > bin/newseq >-bin/noreturn > bin/notseq >-bin/nrscope >+bin/noreturn > bin/nthseq > bin/octanol > bin/oddcomp >@@ -195,7 +111,7 @@ > bin/prophet > bin/prosextract > bin/pscan >-bin/psiblasts >+bin/psiphi > bin/rebaseextract > bin/recoder > bin/redata >@@ -203,9 +119,6 @@ > bin/restover > bin/restrict > bin/revseq >-bin/runJemboss.csh >-bin/scopalign >-bin/scope > bin/seealso > bin/seqmatchall > bin/seqret >@@ -217,144 +130,670 @@ > bin/showseq > bin/shuffleseq > bin/sigcleave >-bin/siggen >-bin/sigscan > bin/silent >+bin/sirna >+bin/sixpack >+bin/skipseq > bin/splitter > bin/stretcher > bin/stssearch > bin/supermatcher >-bin/swissparse > bin/syco >+bin/tcode > bin/textsearch > bin/tfextract > bin/tfm > bin/tfscan > bin/tmap >+bin/tranalign > bin/transeq > bin/trimest > bin/trimseq >+bin/twofeat >+bin/union > bin/vectorstrip > bin/water >+bin/whichdb > bin/wobble > bin/wordcount > bin/wordmatch > bin/wossname >+bin/yank >+bin/runJemboss.csh > etc/emboss.default.sample >-lib/libajax.a >-lib/libajax.la >-lib/libajax.so >+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/ajax.h >+include/ajarch.h >+include/ajdefine.h >+include/ajacd.h >+include/ajalign.h >+include/ajarr.h >+include/ajassert.h >+include/ajbase.h >+include/ajcall.h >+include/ajcod.h >+include/ajdan.h >+include/ajdmx.h >+include/ajdomain.h >+include/ajexcept.h >+include/ajfeat.h >+include/ajfeatdata.h >+include/ajfile.h >+include/ajfmt.h >+include/ajgraph.h >+include/ajgraphxml.h >+include/ajgraphstruct.h >+include/ajhist.h >+include/ajjava.h >+include/ajlist.h >+include/ajmath.h >+include/ajmatrices.h >+include/ajmem.h >+include/ajmess.h >+include/ajnam.h >+include/ajnexus.h >+include/ajpdb.h >+include/ajpdbio.h >+include/ajphylo.h >+include/ajrange.h >+include/ajreg.h >+include/ajreport.h >+include/ajseq.h >+include/ajseqabi.h >+include/ajseqdata.h >+include/ajseqdb.h >+include/ajseqread.h >+include/ajseqtype.h >+include/ajseqwrite.h >+include/ajsort.h >+include/ajstr.h >+include/ajsys.h >+include/ajtable.h >+include/ajtime.h >+include/ajtranslate.h >+include/ajtree.h >+include/ajutil.h >+include/ajvector.h >+include/pcre.h >+include/pcre_chartables.c >+include/pcre_config.h >+include/pcre_get.c >+include/pcre_printint.c >+include/pcre_internal.h >+include/pcreposix.h >+include/emboss.h >+include/embaln.h >+include/embcom.h >+include/embcons.h >+include/embdata.h >+include/embdbi.h >+include/embdmx.h >+include/embest.h >+include/embexit.h >+include/embgotoh.h >+include/embgroup.h >+include/embiep.h >+include/embindex.h >+include/embinit.h >+include/embmat.h >+include/embmisc.h >+include/embmol.h >+include/embnmer.h >+include/embpat.h >+include/embprop.h >+include/embpdb.h >+include/embdomain.h >+include/embsig.h >+include/embread.h >+include/embshow.h >+include/embword.h >+lib/libplplot.so.5 >+lib/libplplot.so >+lib/libplplot.a > lib/libajax.so.1 >-lib/libajaxg.a >-lib/libajaxg.la >-lib/libajaxg.so >+lib/libajax.so >+lib/libajax.a > lib/libajaxg.so.1 >-lib/libnucleus.a >-lib/libnucleus.la >-lib/libnucleus.so >+lib/libajaxg.so >+lib/libajaxg.a > lib/libnucleus.so.1 >-lib/libplplot.a >-lib/libplplot.la >-lib/libplplot.so >-lib/libplplot.so.5 >-share/EMBOSS/acd/abiview.acd >-share/EMBOSS/acd/ajbad.acd >-share/EMBOSS/acd/ajfeatest.acd >-share/EMBOSS/acd/ajtest.acd >-share/EMBOSS/acd/alignwrap.acd >-share/EMBOSS/acd/antigenic.acd >-share/EMBOSS/acd/backtranseq.acd 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>+%%PORTDOCS%%DOCSDIR%%/programs/text/wossname.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/yank.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/aaindexextract.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/abiview.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/antigenic.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/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/clique.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/codcmp.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/consense.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/contacts.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/contml.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/contrast.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/dan.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/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/dnacomp.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnadist.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnainvar.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnaml.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnamlk.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnapars.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dnapenny.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dollop.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/dolpenny.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/domainer.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/eclique.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/econsense.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/econtml.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/econtrast.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednaml.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednacomp.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednadist.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednainvar.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednamlk.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednapars.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ednapenny.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/edollop.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/edolpenny.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/efactor.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/efitch.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/egendist.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/einverted.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/ekitsch.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/embossdata.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/embossversion.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/emix.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/emma.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/emowse.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/eneighbor.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/entret.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/epenny.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/epestfind.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/erestml.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/eprimer3.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/eprotdist.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/eprotpars.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/equicktandem.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/eseqboot.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/factor.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/findkm.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/fitch.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/gendist.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/getorf.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/helixturnhelix.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/hetparse.txt >+%%PORTDOCS%%DOCSDIR%%/programs/text/hmmgen.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%%/tutorials/emboss-gcg.ppt >+%%PORTDOCS%%DOCSDIR%%/tutorials/emboss-interfaces.ppt >+%%PORTDOCS%%DOCSDIR%%/tutorials/emboss-talk.ppt >+%%PORTDOCS%%DOCSDIR%%/tutorials/emboss_tut.tar.gz >+share/EMBOSS/plstnd5.fnt >+share/EMBOSS/plxtnd5.fnt > share/EMBOSS/acd/megamerger.acd > share/EMBOSS/acd/merger.acd > share/EMBOSS/acd/msbar.acd >+share/EMBOSS/acd/mwcontam.acd > share/EMBOSS/acd/mwfilter.acd > share/EMBOSS/acd/needle.acd >+share/EMBOSS/acd/newcoils.acd > share/EMBOSS/acd/newcpgreport.acd > share/EMBOSS/acd/newcpgseek.acd > share/EMBOSS/acd/newseq.acd > share/EMBOSS/acd/noreturn.acd > share/EMBOSS/acd/notseq.acd >-share/EMBOSS/acd/nrscope.acd > share/EMBOSS/acd/nthseq.acd > share/EMBOSS/acd/octanol.acd > share/EMBOSS/acd/oddcomp.acd >@@ -363,7 +802,6 @@ > share/EMBOSS/acd/patmatdb.acd > share/EMBOSS/acd/patmatmotifs.acd > share/EMBOSS/acd/patmattest.acd >-share/EMBOSS/acd/pdbtosp.acd > share/EMBOSS/acd/pepcoil.acd > share/EMBOSS/acd/pepinfo.acd > share/EMBOSS/acd/pepnet.acd >@@ -386,7 +824,6 @@ > share/EMBOSS/acd/prophet.acd > share/EMBOSS/acd/prosextract.acd > share/EMBOSS/acd/pscan.acd >-share/EMBOSS/acd/psiblasts.acd > share/EMBOSS/acd/rebaseextract.acd > share/EMBOSS/acd/recoder.acd > share/EMBOSS/acd/redata.acd >@@ -394,40 +831,37 @@ > share/EMBOSS/acd/restover.acd > share/EMBOSS/acd/restrict.acd > share/EMBOSS/acd/revseq.acd >-share/EMBOSS/acd/scopalign.acd >-share/EMBOSS/acd/scopparse.acd >-share/EMBOSS/acd/scope.acd > share/EMBOSS/acd/seealso.acd > share/EMBOSS/acd/seqinfo.acd > share/EMBOSS/acd/seqmatchall.acd >-share/EMBOSS/acd/seqnr.acd > share/EMBOSS/acd/seqret.acd > share/EMBOSS/acd/seqretall.acd > share/EMBOSS/acd/seqretallfeat.acd > share/EMBOSS/acd/seqretset.acd > share/EMBOSS/acd/seqretsingle.acd > share/EMBOSS/acd/seqretsplit.acd >-share/EMBOSS/acd/seqsort.acd >+share/EMBOSS/acd/seqrettype.acd > share/EMBOSS/acd/showalign.acd > share/EMBOSS/acd/showdb.acd > share/EMBOSS/acd/showfeat.acd > share/EMBOSS/acd/showorf.acd > share/EMBOSS/acd/showseq.acd > share/EMBOSS/acd/shuffleseq.acd >+share/EMBOSS/acd/tfm.acd > share/EMBOSS/acd/sigcleave.acd >-share/EMBOSS/acd/siggen.acd >-share/EMBOSS/acd/sigscan.acd > share/EMBOSS/acd/silent.acd >+share/EMBOSS/acd/sirna.acd >+share/EMBOSS/acd/sixpack.acd >+share/EMBOSS/acd/skipseq.acd > share/EMBOSS/acd/splitter.acd > share/EMBOSS/acd/stretcher.acd > share/EMBOSS/acd/stssearch.acd > share/EMBOSS/acd/supermatcher.acd >-share/EMBOSS/acd/swissparse.acd > share/EMBOSS/acd/syco.acd >+share/EMBOSS/acd/tcode.acd > share/EMBOSS/acd/testplot.acd > share/EMBOSS/acd/textsearch.acd > share/EMBOSS/acd/tfextract.acd >-share/EMBOSS/acd/tfm.acd > share/EMBOSS/acd/tfscan.acd > share/EMBOSS/acd/tmap.acd > share/EMBOSS/acd/tranalign.acd >@@ -435,6 +869,7 @@ > share/EMBOSS/acd/treetypedisplay.acd > share/EMBOSS/acd/trimest.acd > share/EMBOSS/acd/trimseq.acd >+share/EMBOSS/acd/twofeat.acd > share/EMBOSS/acd/union.acd > share/EMBOSS/acd/vectorstrip.acd > share/EMBOSS/acd/water.acd >@@ -444,6 +879,93 @@ > share/EMBOSS/acd/wordmatch.acd > share/EMBOSS/acd/wossname.acd > share/EMBOSS/acd/yank.acd >+share/EMBOSS/acd/codes.english >+share/EMBOSS/acd/groups.standard >+share/EMBOSS/acd/sections.standard >+share/EMBOSS/acd/aaindexextract.acd >+share/EMBOSS/acd/abiview.acd >+share/EMBOSS/acd/ajbad.acd >+share/EMBOSS/acd/ajfeatest.acd >+share/EMBOSS/acd/ajtest.acd >+share/EMBOSS/acd/antigenic.acd >+share/EMBOSS/acd/backtranseq.acd >+share/EMBOSS/acd/banana.acd >+share/EMBOSS/acd/biosed.acd >+share/EMBOSS/acd/btwisted.acd >+share/EMBOSS/acd/cai.acd >+share/EMBOSS/acd/chaos.acd >+share/EMBOSS/acd/charge.acd >+share/EMBOSS/acd/checktrans.acd >+share/EMBOSS/acd/chips.acd >+share/EMBOSS/acd/cirdna.acd >+share/EMBOSS/acd/codcmp.acd >+share/EMBOSS/acd/coderet.acd >+share/EMBOSS/acd/complex.acd >+share/EMBOSS/acd/compseq.acd >+share/EMBOSS/acd/cons.acd >+share/EMBOSS/acd/corbatest.acd >+share/EMBOSS/acd/cpgplot.acd >+share/EMBOSS/acd/cpgreport.acd >+share/EMBOSS/acd/cusp.acd >+share/EMBOSS/acd/cutgextract.acd >+share/EMBOSS/acd/cutseq.acd >+share/EMBOSS/acd/dan.acd >+share/EMBOSS/acd/dbiblast.acd >+share/EMBOSS/acd/dbifasta.acd >+share/EMBOSS/acd/dbiflat.acd >+share/EMBOSS/acd/dbigcg.acd >+share/EMBOSS/acd/degapseq.acd >+share/EMBOSS/acd/demoalign.acd >+share/EMBOSS/acd/demofeatures.acd >+share/EMBOSS/acd/iep.acd >+share/EMBOSS/acd/demolist.acd >+share/EMBOSS/acd/demoreport.acd >+share/EMBOSS/acd/demosequence.acd >+share/EMBOSS/acd/demostring.acd >+share/EMBOSS/acd/demotable.acd >+share/EMBOSS/acd/descseq.acd >+share/EMBOSS/acd/diffseq.acd >+share/EMBOSS/acd/digest.acd >+share/EMBOSS/acd/distmat.acd >+share/EMBOSS/acd/dotmatcher.acd >+share/EMBOSS/acd/dotpath.acd >+share/EMBOSS/acd/dottup.acd >+share/EMBOSS/acd/dreg.acd >+share/EMBOSS/acd/einverted.acd >+share/EMBOSS/acd/embossdata.acd >+share/EMBOSS/acd/embossversion.acd >+share/EMBOSS/acd/emma.acd >+share/EMBOSS/acd/emowse.acd >+share/EMBOSS/acd/entrails.acd >+share/EMBOSS/acd/entret.acd >+share/EMBOSS/acd/epestfind.acd >+share/EMBOSS/acd/eprimer3.acd >+share/EMBOSS/acd/equicktandem.acd >+share/EMBOSS/acd/est2genome.acd >+share/EMBOSS/acd/etandem.acd >+share/EMBOSS/acd/extractseq.acd >+share/EMBOSS/acd/extractfeat.acd >+share/EMBOSS/acd/findkm.acd >+share/EMBOSS/acd/freak.acd >+share/EMBOSS/acd/fuzznuc.acd >+share/EMBOSS/acd/fuzzpro.acd >+share/EMBOSS/acd/fuzztran.acd >+share/EMBOSS/acd/garnier.acd >+share/EMBOSS/acd/geecee.acd >+share/EMBOSS/acd/getorf.acd >+share/EMBOSS/acd/helixturnhelix.acd >+share/EMBOSS/acd/hmoment.acd >+share/EMBOSS/acd/histogramtest.acd >+share/EMBOSS/acd/infoalign.acd >+share/EMBOSS/acd/infoseq.acd >+share/EMBOSS/acd/isochore.acd >+share/EMBOSS/acd/lindna.acd >+share/EMBOSS/acd/listor.acd >+share/EMBOSS/acd/marscan.acd >+share/EMBOSS/acd/maskfeat.acd >+share/EMBOSS/acd/maskseq.acd >+share/EMBOSS/acd/matcher.acd >+share/EMBOSS/data/AAINDEX/dummyfile > share/EMBOSS/data/CODONS/Eacc.cut > share/EMBOSS/data/CODONS/Eadenovirus5.cut > share/EMBOSS/data/CODONS/Eadenovirus7.cut >@@ -491,10 +1013,10 @@ > share/EMBOSS/data/CODONS/Edro_h.cut > share/EMBOSS/data/CODONS/Edrosophila.cut > share/EMBOSS/data/CODONS/Eeca.cut >+share/EMBOSS/data/CODONS/Ef1.cut > share/EMBOSS/data/CODONS/Eeco.cut > share/EMBOSS/data/CODONS/Eeco_h.cut > share/EMBOSS/data/CODONS/Eecoli.cut >-share/EMBOSS/data/CODONS/Ef1.cut > share/EMBOSS/data/CODONS/Efish.cut > share/EMBOSS/data/CODONS/Efmdvpolyp.cut > share/EMBOSS/data/CODONS/Eham.cut >@@ -595,6 +1117,9 @@ > share/EMBOSS/data/CODONS/Eysp.cut > share/EMBOSS/data/CODONS/Ezebrafish.cut > share/EMBOSS/data/CODONS/Ezma.cut >+share/EMBOSS/data/REBASE/dummyfile >+share/EMBOSS/data/PRINTS/dummyfile >+share/EMBOSS/data/PROSITE/dummyfile > share/EMBOSS/data/EBLOSUM30 > share/EMBOSS/data/EBLOSUM35 > share/EMBOSS/data/EBLOSUM40 >@@ -720,203 +1245,21 @@ > share/EMBOSS/data/Etags.pir > share/EMBOSS/data/Etags.protein > share/EMBOSS/data/Etags.swiss >+share/EMBOSS/data/Etcode.dat >+share/EMBOSS/data/Evdw.dat > share/EMBOSS/data/Ewhite-wimley.dat >-share/EMBOSS/data/PRINTS/dummyfile >-share/EMBOSS/data/PROSITE/dummyfile >-share/EMBOSS/data/REBASE/dummyfile > share/EMBOSS/data/embossre.equ >+share/EMBOSS/data/Emwfilter.dat >+share/EMBOSS/data/Emass.dat 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share/EMBOSS/test/embl/entrynam.idx >+share/EMBOSS/test/embl/seqvn.hit >+share/EMBOSS/test/embl/seqvn.trg >+share/EMBOSS/test/embl/des.hit >+share/EMBOSS/test/embl/des.trg >+share/EMBOSS/test/embl/keyword.hit >+share/EMBOSS/test/embl/keyword.trg >+share/EMBOSS/test/embl/taxon.hit >+share/EMBOSS/test/embl/taxon.trg > share/EMBOSS/test/embl/est.dat > share/EMBOSS/test/embl/fun.dat > share/EMBOSS/test/embl/hum1.dat > share/EMBOSS/test/embl/inv.dat >-share/EMBOSS/test/embl/keyword.hit >-share/EMBOSS/test/embl/keyword.trg > share/EMBOSS/test/embl/pln.dat > share/EMBOSS/test/embl/pro.dat > share/EMBOSS/test/embl/rod.dat >-share/EMBOSS/test/embl/seqvn.hit >-share/EMBOSS/test/embl/seqvn.trg > share/EMBOSS/test/embl/sts.dat >-share/EMBOSS/test/embl/taxon.hit >-share/EMBOSS/test/embl/taxon.trg > share/EMBOSS/test/embl/vrl.dat > share/EMBOSS/test/embl/vrt.dat > share/EMBOSS/test/genbank/acnum.hit >@@ -1029,10 +1381,10 @@ > share/EMBOSS/test/gb/htg.seq > share/EMBOSS/test/pir/acnum.hit > 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share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup >-@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser >-@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs >+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap > @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss > @dirrm share/EMBOSS/jemboss/api/org/emboss > @dirrm share/EMBOSS/jemboss/api/org > @dirrm share/EMBOSS/jemboss/api >+@dirrm share/EMBOSS/jemboss/images >+@dirrm share/EMBOSS/jemboss/lib/axis >+@dirrm share/EMBOSS/jemboss/lib >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/editor >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/draw >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap >+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss >+@dirrm share/EMBOSS/jemboss/org/emboss >+@dirrm share/EMBOSS/jemboss/org >+@dirrm share/EMBOSS/jemboss/resources >+@dirrm share/EMBOSS/jemboss/utils > @dirrm share/EMBOSS/jemboss >-@dirrm share/EMBOSS/data/REBASE >-@dirrm share/EMBOSS/data/PROSITE >-@dirrm share/EMBOSS/data/PRINTS >-@dirrm share/EMBOSS/data/CODONS >-@dirrm share/EMBOSS/data >-@dirrm share/EMBOSS/acd > @dirrm share/EMBOSS >diff -ruN /usr/ports/biology/emboss/scripts/configure.emboss emboss/scripts/configure.emboss >--- /usr/ports/biology/emboss/scripts/configure.emboss Fri Aug 3 08:32:42 2001 >+++ emboss/scripts/configure.emboss Wed Dec 31 21:00:00 1969 >@@ -1,73 +0,0 @@ >-#!/bin/sh >- >-if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then >- exit >-fi >- >-if [ "${BATCH}" ]; then >- set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\" >-else >- /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \ >- --checklist "\n\ >-These third party applications have been adapted to >-function as part of EMBOSS.\n >-Please select EMBASSY applications to install:" -1 -1 6 \ >-EMNU "v${EMNU_VERSION} - Text-based menu" ON \ >-HMMER "v${HMMER_VERSION} - HMM alignment" ON \ >-MEME "v${MEME_VERSION} - Motif detection" ON \ >-MSE "v${MSE_VERSION} - Phylogeny inference" ON \ >-PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \ >-TOPO "v${TOPO_VERSION} - Transmembrane display" ON \ >-2> /tmp/checklist.tmp.$$ >- >- retval=$? >- >- if [ -s /tmp/checklist.tmp.$$ ]; then >- set `cat /tmp/checklist.tmp.$$` >- fi >- ${RM} -f /tmp/checklist.tmp.$$ >- >- case $retval in >- 0) >- if [ -z "$*" ]; then >- echo "Nothing selected" >- fi >- ;; >- 1) >- echo "Cancel pressed." >- exit 1 >- ;; >- esac >-fi >- >-${MKDIR} ${WRKDIRPREFIX}${CURDIR} >-exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc >- >-while [ "$1" ]; do >- case $1 in >- \"EMNU\") >- echo "WITH_EMNU= yes" >- ;; >- \"HMMER\") >- echo "WITH_HMMER= yes" >- ;; >- \"MEME\") >- echo "WITH_MEME= yes" >- ;; >- \"MSE\") >- echo "WITH_MSE= yes" >- ;; >- \"PHYLIP\") >- echo "WITH_PHYLIP= yes" >- ;; >- \"TOPO\") >- echo "WITH_TOPO= yes" >- ;; >- *) >- echo "Invalid option(s): $*" > /dev/stderr >- ${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc >- exit 1 >- ;; >- esac >- shift >-done
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