From 7e4beec5d70602585699467ad8b458bdeec03e69 Mon Sep 17 00:00:00 2001 From: "James E. Housley" Date: Mon, 13 Nov 2000 13:48:49 +0000 Subject: - 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. PR: 22818 Submitted by: Johann Visagie MAINTAINER --- biology/emboss/Makefile | 76 ++++++++++++++++++++++++++++++++- biology/emboss/distinfo | 5 ++- biology/emboss/pkg-descr | 13 +++++- biology/emboss/scripts/configure.emboss | 61 ++++++++++++++++++++++++++ 4 files changed, 150 insertions(+), 5 deletions(-) create mode 100644 biology/emboss/scripts/configure.emboss (limited to 'biology') diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 651c403ee3eb..5ffa3f400065 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -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}${EXTRACT_SUFX} MAINTAINER= johann@egenetics.com @@ -20,12 +23,51 @@ LIB_DEPENDS= gd.1:${PORTSDIR}/graphics/gd \ 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 @@ post-patch: ${WRKSRC}/${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 diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index f2d8f7e3d2ef..72b54429db4b 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -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 --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr index 3b212c44b033..37865f30eebe 100644 --- a/biology/emboss/pkg-descr +++ b/biology/emboss/pkg-descr @@ -4,12 +4,21 @@ analysis. EMBOSS is produced by the European Molecular Biology Network (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/ -- Johann Visagie diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss new file mode 100644 index 000000000000..a17b495c50b1 --- /dev/null +++ b/biology/emboss/scripts/configure.emboss @@ -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 -- cgit v1.2.3