Date: Mon, 13 Nov 2000 15:14:00 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/22818: Port update: biology/emboss (MAINTAINER) Message-ID: <E13vJQu-000A6M-00@fling.sanbi.ac.za>
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>Number: 22818 >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: Mon Nov 13 05:20:01 PST 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - This is a fairly extensive rework of this port. - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to choose which of these should be isntalled. - Parts of this has been liberally plagiarised from the www/mod_php4 and textprox/py-xml ports. :-) - New files: - pkg-plist.MSE - pkg-plist.PHYLIP - pkg-plist.TOPO - scripts/configure.emboss - Mainly tested on 5.0-CURRENT. One of the EMBASSY tools - MSE - fails to compile on 3-STABLE and earlier systems due to ncurses version incompatiblities. I'm still working on a workaround. >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Mon Nov 13 14:50:54 2000 +++ emboss/Makefile Mon Nov 13 14:53:31 2000 @@ -7,10 +7,13 @@ PORTNAME= emboss PORTVERSION= 1.7.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ -DISTNAME= EMBOSS-${PORTVERSION} +DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} +DIST_SUBDIR= ${PORTNAME} +EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} MAINTAINER= johann@egenetics.com @@ -20,12 +23,51 @@ USE_GMAKE= yes USE_LIBTOOL= yes USE_XLIB= yes +PLIST= ${WRKDIR}/pkg-plist -CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include/gd" \ +.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc) +.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc" +.endif + +CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \ LIBS="-L${LOCALBASE}/lib" +SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ + MKDIR="${MKDIR}" \ + RM="${RM}" + +WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} +EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY +PHYLIP_VERSION= 3.573c +MSE_VERSION= 0.0.4 +TOPO_VERSION= 0.1 +.for app in MSE PHYLIP TOPO +SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" +.if defined(WITH_${app}) +APPLIST+= ${app} +PLISTS+= ${PKGDIR}/pkg-plist.${app} +${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} +${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} +DISTFILES+= ${${app}_DISTFILE} +.endif +.endfor +PLISTS+= ${PKGDIR}/pkg-plist DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html +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: .for DIR in ${DOC_DIRS} @ ${PERL} -pi.orig -e \ @@ -33,11 +75,41 @@ ${WRKSRC}/${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 + +pre-install: + @ ${CAT} ${PLISTS} > ${PLIST} + post-install: +.for app in ${APPLIST} + @ (cd ${${app}_WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ + ${MAKE_ARGS} ${INSTALL_TARGET}) +.endfor @ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \ ${PREFIX}/etc/emboss.default.sample .if !defined(BATCH) @ ${CAT} ${PKGMESSAGE} .endif + +post-clean: + @ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc .include <bsd.port.mk> diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Mon Nov 13 14:50:54 2000 +++ emboss/distinfo Wed Nov 1 16:22:48 2000 @@ -1 +1,4 @@ -MD5 (EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341 +MD5 (emboss/EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = e41b0552196e9b7b46ca0e9563e9384a +MD5 (emboss/MSE-0.0.4.tar.gz) = 6ba124ff85465be3541d2e250248cd3d +MD5 (emboss/TOPO-0.1.tar.gz) = 687c6ca8ba945520b11058ba28ee880d diff -ruN emboss.bak/pkg-descr emboss/pkg-descr --- emboss.bak/pkg-descr Mon Nov 13 14:50:54 2000 +++ emboss/pkg-descr Mon Nov 13 14:50:24 2000 @@ -4,11 +4,20 @@ (EMBnet - http://www.embnet.org/). All EMBOSS tools are all built around the same set of core libraries - AJAX -and NUCLEUS - and therefore share a unified user interface and a uniform -sequence addressing methodology. +and NUCLEUS - and therefore share a unified user interface, have similar +"look and feel", and implement a uniform sequence addressing methodology. The various components of EMBOSS are distributed under the GPL, except the core libraries which are under the LGPL. + +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 +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 +been renamed. WWW: http://www.uk.embnet.org/Software/EMBOSS/ diff -ruN emboss.bak/pkg-plist.MSE emboss/pkg-plist.MSE --- emboss.bak/pkg-plist.MSE Thu Jan 1 02:00:00 1970 +++ emboss/pkg-plist.MSE Wed Nov 8 15:55:07 2000 @@ -0,0 +1,6 @@ +bin/mse +lib/libckit.a +lib/libckit.la +lib/libckit.so +lib/libckit.so.1 +share/EMBOSS/acd/mse.acd diff -ruN emboss.bak/pkg-plist.PHYLIP emboss/pkg-plist.PHYLIP --- emboss.bak/pkg-plist.PHYLIP Thu Jan 1 02:00:00 1970 +++ emboss/pkg-plist.PHYLIP Wed Nov 8 15:55:26 2000 @@ -0,0 +1,48 @@ +bin/eclique +bin/econsense +bin/econtml +bin/econtrast +bin/ednacomp +bin/ednadist +bin/ednainvar +bin/ednaml +bin/ednamlk +bin/ednapars +bin/ednapenny +bin/edollop +bin/edolpenny +bin/efactor +bin/efitch +bin/egendist +bin/ekitsch +bin/emix +bin/eneighbor +bin/epenny +bin/eprotdist +bin/eprotpars +bin/erestml +bin/eseqboot +share/EMBOSS/acd/eclique.acd +share/EMBOSS/acd/econsense.acd +share/EMBOSS/acd/econtml.acd +share/EMBOSS/acd/econtrast.acd +share/EMBOSS/acd/ednacomp.acd +share/EMBOSS/acd/ednadist.acd +share/EMBOSS/acd/ednainvar.acd +share/EMBOSS/acd/ednaml.acd +share/EMBOSS/acd/ednamlk.acd +share/EMBOSS/acd/ednapars.acd +share/EMBOSS/acd/ednapenny.acd +share/EMBOSS/acd/edollop.acd +share/EMBOSS/acd/edolpenny.acd +share/EMBOSS/acd/efactor.acd +share/EMBOSS/acd/efitch.acd +share/EMBOSS/acd/egendist.acd +share/EMBOSS/acd/ekitsch.acd +share/EMBOSS/acd/emix.acd +share/EMBOSS/acd/eneighbor.acd +share/EMBOSS/acd/epenny.acd +share/EMBOSS/acd/eprotdist.acd +share/EMBOSS/acd/eprotpars.acd +share/EMBOSS/acd/erestml.acd +share/EMBOSS/acd/eseqboot.acd diff -ruN emboss.bak/pkg-plist.TOPO emboss/pkg-plist.TOPO --- emboss.bak/pkg-plist.TOPO Thu Jan 1 02:00:00 1970 +++ emboss/pkg-plist.TOPO Wed Nov 8 15:55:14 2000 @@ -0,0 +1,2 @@ +bin/topo +share/EMBOSS/acd/topo.acd diff -ruN emboss.bak/scripts/configure.emboss emboss/scripts/configure.emboss --- emboss.bak/scripts/configure.emboss Thu Jan 1 02:00:00 1970 +++ emboss/scripts/configure.emboss Mon Nov 13 13:53:34 2000 @@ -0,0 +1,61 @@ +#!/bin/sh + +if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then + exit +fi + +if [ "${BATCH}" ]; then + set \"MSE\" \"PHYLIP\" \"TOPO\" +else + /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \ + --checklist "\n\ +These third party applications have been adapted to +function as part of EMBOSS.\n +Please select EMBASSY applications to install:" -1 -1 3 \ +MSE "v${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 + \"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 >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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