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 15ED713835B for ; Sat, 6 Mar 2021 14:25:22 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 49E30E08A0; Sat, 6 Mar 2021 14:25:21 +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 32AECE08A0 for ; Sat, 6 Mar 2021 14:25:21 +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 ADBEA335DAB for ; Sat, 6 Mar 2021 14:25:19 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 19700585 for ; Sat, 6 Mar 2021 14:25:18 +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: <1615040707.14b1dbd3fe67cddaf19c0502199733077cbd776b.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sga/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/sga/sga-9999.ebuild X-VCS-Directories: sci-biology/sga/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 14b1dbd3fe67cddaf19c0502199733077cbd776b X-VCS-Branch: master Date: Sat, 6 Mar 2021 14:25:18 +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: f394aa18-76ea-4d8b-93b9-a173d6b8eda9 X-Archives-Hash: d8d1f94609b425d0dcb7f5fdface7a03 commit: 14b1dbd3fe67cddaf19c0502199733077cbd776b Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 14:25:07 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 14:25:07 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=14b1dbd3 sci-biology/sga: EAPI bump Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/sga/sga-9999.ebuild | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild index 52f7bb69c..7519b3e2a 100644 --- a/sci-biology/sga/sga-9999.ebuild +++ b/sci-biology/sga/sga-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils git-r3 +inherit git-r3 autotools DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)" HOMEPAGE="https://github.com/jts/sga" @@ -14,20 +14,27 @@ SLOT="0" KEYWORDS="" IUSE="jemalloc python" -DEPEND="dev-cpp/sparsehash +DEPEND=" + dev-cpp/sparsehash sci-biology/bamtools sys-libs/zlib - jemalloc? ( dev-libs/jemalloc )" + jemalloc? ( dev-libs/jemalloc ) +" RDEPEND="${DEPEND} sci-biology/abyss python? ( sci-biology/pysam sci-biology/ruffus )" +S="${WORKDIR}/${P}/src" + +src_prepare() { + default + eautoreconf +} + # http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm src_configure(){ - cd src || die - ./autogen.sh || die - econf --with-bamtools="${EPREFIX}"/usr + econf --with-bamtools="${EPREFIX}"/usr --with-sparsehash="${EPREFIX}"/usr } src_compile(){ @@ -38,12 +45,10 @@ src_compile(){ # # other unreviewed patches: # https://github.com/jts/sga/issues/96 - cd src || die "Try -std=g++-98, try gcc-5 or -std=c++03" default } src_install(){ - cd src || die dodoc README emake install DESTDIR="${D}" insinto /usr/share/sga/examples