diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/emboss/Makefile | 76 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 5 | ||||
| -rw-r--r-- | biology/emboss/pkg-descr | 13 | ||||
| -rw-r--r-- | biology/emboss/scripts/configure.emboss | 61 |
4 files changed, 150 insertions, 5 deletions
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 <bsd.port.mk> 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 <johann@egenetics.com> 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 |