From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 7D2C5138ACF for ; Wed, 4 Feb 2015 08:37:11 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id BA907E09BD; Wed, 4 Feb 2015 08:37:09 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 33A2BE09BD for ; Wed, 4 Feb 2015 08:37:09 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 3FF673407DA for ; Wed, 4 Feb 2015 08:37:08 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 31A8011065 for ; Wed, 4 Feb 2015 08:37:06 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1423037157.1f18e25a472d14585102cdf0fc2819fdf8090bc0.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: eclass/, sci-biology/emboss/, sci-biology/emboss/files/ X-VCS-Repository: proj/sci X-VCS-Files: eclass/emboss-r1.eclass eclass/emboss.eclass sci-biology/emboss/emboss-6.6.0.ebuild sci-biology/emboss/files/README.gentoo X-VCS-Directories: sci-biology/emboss/ eclass/ sci-biology/emboss/files/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 1f18e25a472d14585102cdf0fc2819fdf8090bc0 X-VCS-Branch: master Date: Wed, 4 Feb 2015 08:37:06 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 5509a853-7537-4b22-b90e-a74c181941ee X-Archives-Hash: f3db5b303a1391034a1903c19c19096b commit: 1f18e25a472d14585102cdf0fc2819fdf8090bc0 Author: Justin Lecher gentoo org> AuthorDate: Wed Feb 4 07:56:01 2015 +0000 Commit: Justin Lecher gentoo org> CommitDate: Wed Feb 4 08:05:57 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1f18e25a Rename eclass to compensate API changes * Require at least EAPI=5 * Clean tiny bits Signed-off-by: Justin Lecher gentoo.org> --- eclass/{emboss.eclass => emboss-r1.eclass} | 28 ++++++++++-------------- sci-biology/emboss/emboss-6.6.0.ebuild | 25 +++++++++------------- sci-biology/emboss/files/README.gentoo | 34 ++++++++++++++++++++++++++++++ 3 files changed, 55 insertions(+), 32 deletions(-) diff --git a/eclass/emboss.eclass b/eclass/emboss-r1.eclass similarity index 85% rename from eclass/emboss.eclass rename to eclass/emboss-r1.eclass index 3ba65bb..b185802 100644 --- a/eclass/emboss.eclass +++ b/eclass/emboss-r1.eclass @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -# @ECLASS: emboss.eclass +# @ECLASS: emboss-r1.eclass # @MAINTAINER: # sci-biology@gentoo.org # jlec@gentoo.org @@ -13,14 +13,13 @@ # Next gen author: Ted Tanberry # @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons). # @DESCRIPTION: -# The inheriting ebuild must set at least EAPI=4 and provide EBO_DESCRIPTION before the inherit line. +# The inheriting ebuild must set at least EAPI=5 and provide EBO_DESCRIPTION before the inherit line. # KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard # ebuild variables can be extended (FOO+=" bar"). -# Default installation of following DOCS=() # # Example: # -# EAPI="4" +# EAPI="5" # # EBO_DESCRIPTION="applications from the CBS group" # @@ -42,8 +41,8 @@ # Extra config options passed to econf, similar to EXTRA_ECONF. case ${EAPI:-0} in - 4|5) ;; - *) die "this eclass doesn't support < EAPI 4" ;; + 5) ;; + *) die "this eclass doesn't support < EAPI 5" ;; esac if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then @@ -85,26 +84,23 @@ if [[ ${PN} == embassy-* ]]; then S="${WORKDIR}"/${EF} fi -DOCS=() - # @FUNCTION: emboss_src_prepare # @DESCRIPTION: # Does the following things # # 1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present, # and eventually runs eautoreconf in autotools-utils -# 2. Patches with "${WORKDIR}"/${P}-upstream-r1.patch, if ${EBO_PATCH} is set -# 3. Patches with "${FILESDIR}"/${PF}.patch, if present +# 2. Patches with "${FILESDIR}"/${PF}.patch, if present +# 3. Applies ${PATCHES[@]} via autotools-utils.eclass # -emboss_src_prepare() { +emboss-r1_src_prepare() { if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then mv configure.{in,ac} || die epatch "${FILESDIR}"/${P}_fix-build-system.patch fi - [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream-r1.patch - [[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch + [[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch autotools-utils_src_prepare } @@ -125,14 +121,13 @@ emboss_src_prepare() { # --docdir="${EPREFIX}/usr/share/doc/${PF}" # ${EBO_EXTRA_ECONF} -emboss_src_configure() { +emboss-r1_src_configure() { local myeconfargs=( $(use_with X x) $(use_with png pngdriver "${EPREFIX}/usr") $(use_with pdf hpdf "${EPREFIX}/usr") $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") - $(use_enable static-libs static) --enable-large --without-java --enable-systemlibs @@ -140,9 +135,8 @@ emboss_src_configure() { ${EBO_EXTRA_ECONF} ) - if [[ ${EMBASSY_PACKAGE} == yes ]]; then + [[ ${EMBASSY_PACKAGE} == yes ]] && \ append-cppflags "-I${EPREFIX}/usr/include/emboss" - fi autotools-utils_src_configure } diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild index 7ac75b6..59285d7 100644 --- a/sci-biology/emboss/emboss-6.6.0.ebuild +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -4,10 +4,7 @@ EAPI=5 -inherit autotools-utils emboss eutils - -EBO_PATCH="" -EBOV=${PV} +inherit autotools-utils emboss-r1 eutils readme.gentoo DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" @@ -25,38 +22,36 @@ PDEPEND+=" sci-biology/rebase )" -S="${WORKDIR}"/EMBOSS-${EBOV} - -EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss" +S="${WORKDIR}"/EMBOSS-${PV} DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) + PATCHES=( - "${FILESDIR}/${P}_FORTIFY_SOURCE-fix.patch" - "${FILESDIR}/${P}_plplot-declarations.patch" - "${FILESDIR}/${P}_qa-implicit-declarations.patch" + "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch + "${FILESDIR}"/${P}_plplot-declarations.patch + "${FILESDIR}"/${P}_qa-implicit-declarations.patch ) src_install() { # Use autotools-utils_* to remove useless *.la files autotools-utils_src_install - sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ - dodoc README.Gentoo + readme.gentoo_create_doc # Install env file for setting libplplot and acd files path. - cat <<- EOF > 22emboss + cat > 22emboss <<- EOF # ACD files location EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" EOF doenvd 22emboss - # Remove useless dummy files from the image. + # Remove useless dummy files find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.Gentoo". + # bug #115446). This change is documented in "README.gentoo". mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." } diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo new file mode 100644 index 0000000..d1879bd --- /dev/null +++ b/sci-biology/emboss/files/README.gentoo @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ