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 TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 62CBC158087 for ; Tue, 25 Jan 2022 14:24:30 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 63A7DE01E4; Tue, 25 Jan 2022 14:24:29 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id BDA02E0101 for ; Tue, 25 Jan 2022 14:24:28 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A962F342E2D for ; Tue, 25 Jan 2022 14:24:27 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 18D39275 for ; Tue, 25 Jan 2022 14:24:26 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1643120658.34773140d758b76b35f70f857f7b27ee06503921.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SPAdes/SPAdes-3.15.1.ebuild sci-biology/SPAdes/SPAdes-3.15.3.ebuild X-VCS-Directories: sci-biology/SPAdes/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 34773140d758b76b35f70f857f7b27ee06503921 X-VCS-Branch: master Date: Tue, 25 Jan 2022 14:24:26 +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: ca2f993d-fcde-4a61-a8dd-e3d68dbbd5b3 X-Archives-Hash: c623ed4b7613c8a6ebf3d790cff989c5 commit: 34773140d758b76b35f70f857f7b27ee06503921 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 25 14:24:18 2022 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 25 14:24:18 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34773140 sci-biology/SPAdes: bump to 3.15.3 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 55 --------------------------------- sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 36 +++++++++++++++++++++ 2 files changed, 36 insertions(+), 55 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild deleted file mode 100644 index 853524984..000000000 --- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="https://cab.spbu.ru/software/spades" -SRC_URI=" - https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz - https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - dev-python/regex" -RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" -# BUG: -# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, -# not *.so or *.a are even used) -# -# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their -# existing packages -# nlopt -# llvm -# python_libs -# bamtools -# ConsensusCore -# ssw -# jemalloc -# htrie -# getopt_pp -# cppformat -# cityhash -# samtools -# bwa - -# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? -# bwa-0.7.12 -# bwa-0.6.2 - -src_compile(){ - PREFIX="${ED}"/usr ./spades_compile.sh || die -} - -src_install(){ - # BUG: move *.py files to standard site-packages/ subdirectories - insinto /usr/share/"${PN}" - dodoc "${DISTDIR}"/${P}_*manual.html -} diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild new file mode 100644 index 000000000..553c21e21 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +inherit python-single-r1 + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +HOMEPAGE="https://cab.spbu.ru/software/spades" +SRC_URI=" + https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz + https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html + https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex + ${PYTHON_DEPS} +" +RDEPEND="${DEPEND}" +BDEPEND="dev-util/cmake" + +src_install(){ + einstalldocs + # WORKAROUND: This script does both compile and install in one go + PREFIX="${ED}"/usr ./spades_compile.sh || die +}