diff options
| author | Sergey Matveychuk <sem@FreeBSD.org> | 2004-11-26 01:11:43 +0000 |
|---|---|---|
| committer | Sergey Matveychuk <sem@FreeBSD.org> | 2004-11-26 01:11:43 +0000 |
| commit | 626e4b86a80bda267ca73fe79e9f7883b66b7a1c (patch) | |
| tree | a64a33406a7e567a415937948a405f68a18e2367 /biology/emboss | |
| parent | 6387140db2d9c15715ca845407639eff8d3767ef (diff) | |
| download | ports-626e4b86a80bda267ca73fe79e9f7883b66b7a1c.tar.gz ports-626e4b86a80bda267ca73fe79e9f7883b66b7a1c.zip | |
Notes
Diffstat (limited to 'biology/emboss')
| -rw-r--r-- | biology/emboss/Makefile | 128 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 9 | ||||
| -rw-r--r-- | biology/emboss/files/patch-aa | 26 | ||||
| -rw-r--r-- | biology/emboss/files/patch-ajax::ajjava.c | 11 | ||||
| -rw-r--r-- | biology/emboss/files/patch-configure | 11 | ||||
| -rw-r--r-- | biology/emboss/files/patch-emboss-emboss.default.template | 38 | ||||
| -rw-r--r-- | biology/emboss/pkg-message | 3 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist | 3145 | ||||
| -rw-r--r-- | biology/emboss/scripts/configure.emboss | 73 |
9 files changed, 1632 insertions, 1812 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index c7d8b55f1fd9..18ad062199d2 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,137 +6,55 @@ # 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}" +DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U} +DATADIR= ${PREFIX}/share/${PORTNAME:U} -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 --git a/biology/emboss/distinfo b/biology/emboss/distinfo index bcc2cea1e109..5c53ea980ba9 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -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 --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa deleted file mode 100644 index 60853ff96c11..000000000000 --- a/biology/emboss/files/patch-aa +++ /dev/null @@ -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 $(PREFIX)_ROOT/../emboss.default */ -+ -+ if (!prefixRootFile) -+ { -+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", -+ namInstallRoot, prefix); -+ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); -+ } -+ - if (namFileOrig) - (void) ajStrAppC (&namFileOrig, ", "); - (void) ajStrApp (&namFileOrig, namRootStr); diff --git a/biology/emboss/files/patch-ajax::ajjava.c b/biology/emboss/files/patch-ajax::ajjava.c deleted file mode 100644 index 76189b95c03b..000000000000 --- a/biology/emboss/files/patch-ajax::ajjava.c +++ /dev/null @@ -1,11 +0,0 @@ ---- ajax/ajjava.c.orig Thu May 2 22:06:08 2002 -+++ ajax/ajjava.c Sun May 26 09:14:20 2002 -@@ -75,7 +75,7 @@ - #endif - - #ifndef __ppc__ --#include <crypt.h> -+#include <unistd.h> - #endif - - diff --git a/biology/emboss/files/patch-configure b/biology/emboss/files/patch-configure deleted file mode 100644 index da46a3c60faa..000000000000 --- a/biology/emboss/files/patch-configure +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.orig Mon Jan 22 23:28:17 2001 -+++ configure Thu Jan 25 19:07:33 2001 -@@ -1473,7 +1473,7 @@ - - - --AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\"" - - #AC_PROG_CXX - for ac_prog in mawk gawk nawk awk diff --git a/biology/emboss/files/patch-emboss-emboss.default.template b/biology/emboss/files/patch-emboss-emboss.default.template deleted file mode 100644 index 3bbe6641a0d1..000000000000 --- a/biology/emboss/files/patch-emboss-emboss.default.template +++ /dev/null @@ -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 --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message index 31845abb7690..1c36c80c0b39 100644 --- a/biology/emboss/pkg-message +++ b/biology/emboss/pkg-message @@ -15,7 +15,8 @@ A .embossrc in a user's home directory overrides settings in the 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 --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 7db872665c01..ce1ef92d70f0 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -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/codcmp bin/coderet bin/compseq bin/cons -bin/contacts bin/cpgplot bin/cpgreport bin/cusp @@ -117,11 +32,9 @@ bin/dbiflat bin/dbigcg bin/degapseq bin/descseq -bin/dichet bin/diffseq bin/digest bin/distmat -bin/domainer bin/dotmatcher bin/dotpath bin/dottup @@ -132,6 +45,7 @@ bin/embossversion bin/emma bin/emowse bin/entret +bin/epestfind bin/eprimer3 bin/equicktandem bin/est2genome @@ -151,7 +65,6 @@ bin/hmoment bin/iep bin/infoalign bin/infoseq -bin/interface bin/isochore bin/jembossctl bin/lindna @@ -163,14 +76,14 @@ bin/matcher 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 @@ -178,7 +91,6 @@ bin/palindrome bin/pasteseq bin/patmatdb bin/patmatmotifs -bin/pdbtosp bin/pepcoil bin/pepinfo bin/pepnet @@ -199,7 +111,7 @@ bin/prophecy bin/prophet bin/prosextract bin/pscan -bin/psiblasts +bin/psiphi bin/rebaseextract bin/recoder bin/redata @@ -207,16 +119,10 @@ bin/remap bin/restover bin/restrict bin/revseq -bin/runJemboss.csh -bin/scopalign -bin/scope -bin/scopparse bin/seealso bin/seqmatchall -bin/seqnr bin/seqret bin/seqretsplit -bin/seqsort bin/showalign bin/showdb bin/showfeat @@ -224,15 +130,16 @@ bin/showorf 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 @@ -242,6 +149,7 @@ bin/tranalign bin/transeq bin/trimest bin/trimseq +bin/twofeat bin/union bin/vectorstrip bin/water @@ -251,1441 +159,1598 @@ 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 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+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java +%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java +%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java +%%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/PlafMacros.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/OutputSequenceAttributes.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/SequenceFilter.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java +%%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultList.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java +%%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java +%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java +%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java +%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java +%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java +%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java +%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java +%%DATADIR%%/jemboss/resources/jemboss.properties +%%DATADIR%%/jemboss/resources/readme.html +%%DATADIR%%/jemboss/resources/readmeAlign.html +%%DATADIR%%/jemboss/resources/readmeDNADraw.html +%%DATADIR%%/jemboss/resources/results.html +%%DATADIR%%/jemboss/resources/version +%%DATADIR%%/jemboss/resources/filemgr.html +%%DATADIR%%/jemboss/resources/seqList.html +%%DATADIR%%/jemboss/utils/install-jemboss-server.sh +%%DATADIR%%/jemboss/utils/keys.sh +%%DATADIR%%/jemboss/utils/makeJar.csh +%%DATADIR%%/jemboss/utils/makeJNLP.sh +%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh +%%DATADIR%%/jemboss/utils/template.html +%%DATADIR%%/jemboss/utils/README +%%DATADIR%%/jemboss/LICENSE +%%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 %%DATADIR%%/acd +@dirrm %%DATADIR%%/data/AAINDEX +@dirrm %%DATADIR%%/data/CODONS +@dirrm %%DATADIR%%/data/REBASE +@dirrm %%DATADIR%%/data/PRINTS +@dirrm %%DATADIR%%/data/PROSITE +@dirrm %%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 +@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 +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap +@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss +@dirrm %%DATADIR%%/jemboss/api/org/emboss +@dirrm %%DATADIR%%/jemboss/api/org +@dirrm %%DATADIR%%/jemboss/api +@dirrm %%DATADIR%%/jemboss/images +@dirrm %%DATADIR%%/jemboss/lib/axis +@dirrm %%DATADIR%%/jemboss/lib +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap +@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss +@dirrm %%DATADIR%%/jemboss/org/emboss +@dirrm %%DATADIR%%/jemboss/org +@dirrm %%DATADIR%%/jemboss/resources +@dirrm %%DATADIR%%/jemboss/utils +@dirrm %%DATADIR%%/jemboss +@dirrm %%DATADIR%% diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss deleted file mode 100644 index b14bb8e85d8b..000000000000 --- a/biology/emboss/scripts/configure.emboss +++ /dev/null @@ -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 |