From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 65E84138359 for ; Tue, 22 Sep 2020 11:12:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 42A1BE085B; Tue, 22 Sep 2020 11:12:26 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 16265E085B for ; Tue, 22 Sep 2020 11:12:26 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id D99F0340DC4 for ; Tue, 22 Sep 2020 11:12:23 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 560A7365 for ; Tue, 22 Sep 2020 11:12:22 +0000 (UTC) From: "Aisha Tammy" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Aisha Tammy" Message-ID: <1600771561.cd2304b0b4b65067df0d3ca9a117696f416b01ac.epsilon-0@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/augustus/augustus-3.3.2.ebuild sci-biology/augustus/metadata.xml X-VCS-Directories: sci-biology/augustus/ X-VCS-Committer: epsilon-0 X-VCS-Committer-Name: Aisha Tammy X-VCS-Revision: cd2304b0b4b65067df0d3ca9a117696f416b01ac X-VCS-Branch: master Date: Tue, 22 Sep 2020 11:12:22 +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-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: d8f4603c-bff2-433e-b8d5-4b91b36876c2 X-Archives-Hash: dda1edcb5b9ea2b1d032f0185e8aa9be commit: cd2304b0b4b65067df0d3ca9a117696f416b01ac Author: Aisha Tammy aisha cc> AuthorDate: Tue Sep 22 10:44:43 2020 +0000 Commit: Aisha Tammy aisha cc> CommitDate: Tue Sep 22 10:46:01 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cd2304b0 sci-biology/augustus: drop package present in ::gentoo Package-Manager: Portage-3.0.7, Repoman-3.0.1 Signed-off-by: Aisha Tammy aisha.cc> sci-biology/augustus/augustus-3.3.2.ebuild | 115 ----------------------------- sci-biology/augustus/metadata.xml | 12 --- 2 files changed, 127 deletions(-) diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild deleted file mode 100644 index a959252a0..000000000 --- a/sci-biology/augustus/augustus-3.3.2.ebuild +++ /dev/null @@ -1,115 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit eutils toolchain-funcs - -DESCRIPTION="Eukaryotic gene predictor" -HOMEPAGE="http://bioinf.uni-greifswald.de/augustus - https://github.com/Gaius-Augustus/Augustus" -SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/${PV}.tar.gz -> ${P}.tar.gz" - -# LICENSE="GPL-3" -# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT -# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="bam2wig examples man mysql sqlite" - -RDEPEND=" - bam2wig? ( sci-biology/samtools:0.1-legacy ) - sci-biology/bamtools - >=sci-mathematics/lpsolve-5.5 - sci-libs/gsl - sci-libs/suitesparse - sqlite? ( dev-db/sqlite:3 ) - mysql? ( dev-db/mysql++ ) - >=dev-libs/boost-1.49.0 - sys-libs/zlib" -DEPEND="${RDEPEND} - sys-devel/flex" -S="${WORKDIR}/Augustus-${PV}" - -src_prepare() { - # TODO: do we need anything from the 2.5.5 patch? - # epatch "${FILESDIR}"/${P}-sane-build.patch - default - tc-export CC CXX - # lets respect upstream's wish and keep -ggdb - sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die - sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \ - -i auxprogs/bam2wig/Makefile || die - sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" \ - -i auxprogs/bam2wig/Makefile || die - # https://github.com/Gaius-Augustus/Augustus/issues/53 - sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile || die - sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die - # enable comparative gene prediction (CGP, needs c++11 compiler), - # this needs sci-mathematics/lpsolve - sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die - # enable compressed gzip input - sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die - # comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite - # supposedly pick only either a single-one - if use mysql; then - sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die - elif use sqlite; then - # comparative (mutli-species, CGP) AUGUSTUS with SQLite - sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die - fi - # respect $EPREFIX in all Makefile's - find . -name Makefile | while read f; do \ - sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die; - done -} - -src_compile() { - emake clean && default - - # compile stuff not compiled by default - # https://github.com/Gaius-Augustus/Augustus/issues/52 - cd auxprogs/aln2wig || die - emake -} - -src_install() { - dobin bin/* - - exeinto /usr/libexec/${PN} - doexe scripts/*.{pl,pm,py} scripts/checkUTR - insinto /usr/libexec/${PN} - doins scripts/*.conf - - insinto /usr/share/${PN} - doins -r config - - echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" - doenvd "${S}/99${PN}" - - insinto /usr/libexec/${PN}/gbrowse - doins scripts/gbrowse.conf - insinto /usr/libexec/${PN}/gfftools - doins scripts/gff2ps_mycustom # config setting - - dodoc README.md README-cgp.txt HISTORY.TXT auxprogs/homGeneMapping/README.TXT - dodoc -r docs/*.{pdf,txt} - - if use examples; then - insinto /usr/share/${PN}/ - doins -r docs/tutorial examples - fi - - use man && doman mansrc/*.1 - - # install stuff compiled but not written into bin/ - # https://github.com/Gaius-Augustus/Augustus/issues/14 - dobin auxprogs/utrrnaseq/Debug/utrrnaseq - dodoc auxprogs/utrrnaseq/doc/reference.pdf - # https://github.com/Gaius-Augustus/Augustus/issues/51 - dobin auxprogs/checkTargetSortedness/checkTargetSortedness \ - auxprogs/compileSpliceCands/compileSpliceCands - - # ./augustus-training/ contains web application and setup -} diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml deleted file mode 100644 index 6b4a3e5b5..000000000 --- a/sci-biology/augustus/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - install preformatted manual pages - compile and install bam2wig conversion utility - -