Date: Wed, 24 Jan 2001 11:51:51 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24597: Port update: biology/emboss (MAINTAINER) Message-ID: <E14LMal-0006YS-00@fling.sanbi.ac.za>
next in thread | raw e-mail | index | archive | help
>Number: 24597 >Category: ports >Synopsis: Port update: biology/emboss (MAINTAINER) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Jan 24 02:00:01 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update the EMBOSS suite (biology/emboss) from 1.8.0 to 1.9.0 - Add a new EMBASSY application to the port: EMNU 1.0.2 - File added: pkg-plist.EMNU >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Wed Jan 24 11:48:16 2001 +++ emboss/Makefile Wed Jan 24 11:47:03 2001 @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.8.0 +PORTVERSION= 1.9.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ @@ -23,6 +23,7 @@ USE_GMAKE= yes USE_LIBTOOL= yes USE_XLIB= yes +USE_MOTIF= yes PLIST= ${WRKDIR}/pkg-plist PKGMESSAGE= ${WRKDIR}/pkg-message @@ -31,7 +32,7 @@ .endif CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \ - LIBS="-L${LOCALBASE}/lib" + LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib" SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ MKDIR="${MKDIR}" \ @@ -39,10 +40,11 @@ WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -PHYLIP_VERSION= 3.573c +EMNU_VERSION= 1.0.2 MSE_VERSION= 0.0.4 TOPO_VERSION= 0.1 -.for app in MSE PHYLIP TOPO +PHYLIP_VERSION= 3.573c +.for app in EMNU MSE PHYLIP TOPO SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" .if defined(WITH_${app}) APPLIST+= ${app} diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Wed Jan 24 11:48:16 2001 +++ emboss/distinfo Tue Jan 23 18:22:22 2001 @@ -1,4 +1,5 @@ -MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4f4b54f5e2c3e053baaffb19f258ad2a -MD5 (emboss/MSE-0.0.4.tar.gz) = 0585be481f33eb71ceadee89b339f86e -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 7186d27d0909ffb5481720ec41d99222 -MD5 (emboss/TOPO-0.1.tar.gz) = a8709a31b1fc2f5914365d87b7120e72 +MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c +MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b +MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f +MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3 +MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29 diff -ruN emboss.bak/pkg-descr emboss/pkg-descr --- emboss.bak/pkg-descr Wed Jan 24 11:48:16 2001 +++ emboss/pkg-descr Tue Jan 23 11:56:20 2001 @@ -12,8 +12,8 @@ EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution -for licensing or other reasons. This port includes the three currently -available EMBASSY applications - MSE, PHYLIP and TOPO. During an interactive +for licensing or other reasons. This port includes the currently available +EMBASSY applications - EMNU, MSE, PHYLIP and TOPO. During an interactive install the user will be asked to choose which of these will be installed (default: all). Note that the EMBASSY version of PHYLIP should not clash with the standalone Phylip application due to the fact that its binaries have diff -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Wed Jan 24 11:48:16 2001 +++ emboss/pkg-plist Tue Jan 23 12:33:03 2001 @@ -1,3 +1,4 @@ +bin/abiview bin/acdc bin/antigenic bin/backtranseq @@ -61,6 +62,7 @@ bin/newcpgseek bin/newseq bin/noreturn +bin/notseq bin/nthseq bin/octanol bin/oddcomp @@ -90,8 +92,10 @@ bin/prosextract bin/pscan bin/rebaseextract +bin/recode bin/redata bin/remap +bin/restover bin/restrict bin/revseq bin/seealso @@ -138,6 +142,7 @@ lib/libplplot.a lib/libplplot.so lib/libplplot.so.4 +share/EMBOSS/acd/abiview.acd share/EMBOSS/acd/ajbad.acd share/EMBOSS/acd/ajfeatest.acd share/EMBOSS/acd/ajtest.acd @@ -215,6 +220,7 @@ share/EMBOSS/acd/newcpgseek.acd share/EMBOSS/acd/newseq.acd share/EMBOSS/acd/noreturn.acd +share/EMBOSS/acd/notseq.acd share/EMBOSS/acd/nthseq.acd share/EMBOSS/acd/octanol.acd share/EMBOSS/acd/oddcomp.acd @@ -247,8 +253,10 @@ share/EMBOSS/acd/proteinmotifsearch.acd share/EMBOSS/acd/pscan.acd share/EMBOSS/acd/rebaseextract.acd +share/EMBOSS/acd/recode.acd share/EMBOSS/acd/redata.acd share/EMBOSS/acd/remap.acd +share/EMBOSS/acd/restover.acd share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd share/EMBOSS/acd/scope.acd @@ -468,7 +476,11 @@ share/EMBOSS/data/EGC.13 share/EMBOSS/data/EGC.14 share/EMBOSS/data/EGC.15 +share/EMBOSS/data/EGC.16 share/EMBOSS/data/EGC.2 +share/EMBOSS/data/EGC.21 +share/EMBOSS/data/EGC.22 +share/EMBOSS/data/EGC.23 share/EMBOSS/data/EGC.3 share/EMBOSS/data/EGC.4 share/EMBOSS/data/EGC.5 @@ -660,11 +672,15 @@ share/doc/EMBOSS/manuals/admin.tex share/doc/EMBOSS/manuals/program.ps.gz share/doc/EMBOSS/programs/html/SITE-DIRECTED.html +share/doc/EMBOSS/programs/html/abi_trace_files_group.html +share/doc/EMBOSS/programs/html/abiview.html +share/doc/EMBOSS/programs/html/abiview0.gif share/doc/EMBOSS/programs/html/alignment_global_group.html share/doc/EMBOSS/programs/html/alignment_group.html share/doc/EMBOSS/programs/html/alignment_local_group.html share/doc/EMBOSS/programs/html/alignment_multiple_group.html share/doc/EMBOSS/programs/html/antigenic.html +share/doc/EMBOSS/programs/html/assorted_group.html share/doc/EMBOSS/programs/html/backtranseq.html share/doc/EMBOSS/programs/html/banana.html share/doc/EMBOSS/programs/html/banana0.gif @@ -743,6 +759,7 @@ share/doc/EMBOSS/programs/html/embossdata.html share/doc/EMBOSS/programs/html/emix.html share/doc/EMBOSS/programs/html/emma.html +share/doc/EMBOSS/programs/html/emnu.html share/doc/EMBOSS/programs/html/emowse.html share/doc/EMBOSS/programs/html/eneighbor.html share/doc/EMBOSS/programs/html/entret.html @@ -783,6 +800,7 @@ share/doc/EMBOSS/programs/html/maskseq.html share/doc/EMBOSS/programs/html/matcher.html share/doc/EMBOSS/programs/html/megamerger.html +share/doc/EMBOSS/programs/html/menus_group.html share/doc/EMBOSS/programs/html/merger.html share/doc/EMBOSS/programs/html/mix.html share/doc/EMBOSS/programs/html/motifs_group.html @@ -796,6 +814,7 @@ share/doc/EMBOSS/programs/html/newcpgseek.html share/doc/EMBOSS/programs/html/newseq.html share/doc/EMBOSS/programs/html/noreturn.html +share/doc/EMBOSS/programs/html/notseq.html share/doc/EMBOSS/programs/html/nthseq.html share/doc/EMBOSS/programs/html/octanol.html share/doc/EMBOSS/programs/html/octanol0.gif @@ -843,14 +862,15 @@ share/doc/EMBOSS/programs/html/protein_sequence_features_group.html share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html share/doc/EMBOSS/programs/html/pscan.html +share/doc/EMBOSS/programs/html/re_group.html share/doc/EMBOSS/programs/html/rebaseextract.html +share/doc/EMBOSS/programs/html/recode.html share/doc/EMBOSS/programs/html/redata.html share/doc/EMBOSS/programs/html/reformatting_group.html share/doc/EMBOSS/programs/html/remap.html share/doc/EMBOSS/programs/html/repeats_group.html share/doc/EMBOSS/programs/html/restml.html share/doc/EMBOSS/programs/html/restrict.html -share/doc/EMBOSS/programs/html/restriction_enzymes_group.html share/doc/EMBOSS/programs/html/revseq.html share/doc/EMBOSS/programs/html/secondary_structure_group.html share/doc/EMBOSS/programs/html/seealso.html @@ -864,6 +884,7 @@ share/doc/EMBOSS/programs/html/sequence_composition_group.html share/doc/EMBOSS/programs/html/sequence_display_group.html share/doc/EMBOSS/programs/html/sequence_editing_group.html +share/doc/EMBOSS/programs/html/sequence_features_group.html share/doc/EMBOSS/programs/html/sequence_information_group.html share/doc/EMBOSS/programs/html/showdb.html share/doc/EMBOSS/programs/html/showfeat.html @@ -904,6 +925,7 @@ share/doc/EMBOSS/programs/html/wordmatch.html share/doc/EMBOSS/programs/html/wossname.html share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt +share/doc/EMBOSS/programs/text/abiview.txt share/doc/EMBOSS/programs/text/antigenic.txt share/doc/EMBOSS/programs/text/backtranseq.txt share/doc/EMBOSS/programs/text/banana.txt @@ -967,6 +989,7 @@ share/doc/EMBOSS/programs/text/embossdata.txt share/doc/EMBOSS/programs/text/emix.txt share/doc/EMBOSS/programs/text/emma.txt +share/doc/EMBOSS/programs/text/emnu.txt share/doc/EMBOSS/programs/text/emowse.txt share/doc/EMBOSS/programs/text/eneighbor.txt share/doc/EMBOSS/programs/text/entret.txt @@ -1010,6 +1033,7 @@ share/doc/EMBOSS/programs/text/newcpgseek.txt share/doc/EMBOSS/programs/text/newseq.txt share/doc/EMBOSS/programs/text/noreturn.txt +share/doc/EMBOSS/programs/text/notseq.txt share/doc/EMBOSS/programs/text/nthseq.txt share/doc/EMBOSS/programs/text/octanol.txt share/doc/EMBOSS/programs/text/oddcomp.txt @@ -1041,6 +1065,7 @@ share/doc/EMBOSS/programs/text/protdist.txt share/doc/EMBOSS/programs/text/pscan.txt share/doc/EMBOSS/programs/text/rebaseextract.txt +share/doc/EMBOSS/programs/text/recode.txt share/doc/EMBOSS/programs/text/redata.txt share/doc/EMBOSS/programs/text/remap.txt share/doc/EMBOSS/programs/text/restml.txt diff -ruN emboss.bak/pkg-plist.EMNU emboss/pkg-plist.EMNU --- emboss.bak/pkg-plist.EMNU Thu Jan 1 02:00:00 1970 +++ emboss/pkg-plist.EMNU Wed Jan 24 10:16:46 2001 @@ -0,0 +1,2 @@ +bin/emnu +share/EMBOSS/acd/emnu.acd diff -ruN emboss.bak/scripts/configure.emboss emboss/scripts/configure.emboss --- emboss.bak/scripts/configure.emboss Wed Jan 24 11:48:16 2001 +++ emboss/scripts/configure.emboss Tue Jan 23 19:03:35 2001 @@ -5,13 +5,14 @@ fi if [ "${BATCH}" ]; then - set \"MSE\" \"PHYLIP\" \"TOPO\" + set \"EMNU\" \"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 3 \ +Please select EMBASSY applications to install:" -1 -1 4 \ +EMNU "v${EMNU_VERSION} - Text-based menu" ON \ MSE "v${MSE_VERSION} - Phylogeny inference" ON \ PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \ TOPO "v${TOPO_VERSION} - Transmembrane display" ON \ @@ -42,6 +43,9 @@ while [ "$1" ]; do case $1 in + \"EMNU\") + echo "WITH_EMNU= yes" + ;; \"MSE\") echo "WITH_MSE= yes" ;; >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?E14LMal-0006YS-00>