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 BD4A213835B for ; Sat, 6 Mar 2021 11:55:40 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id ACCF8E0867; Sat, 6 Mar 2021 11:55:39 +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 93453E0867 for ; Sat, 6 Mar 2021 11:55:39 +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 CACDE33BEBB for ; Sat, 6 Mar 2021 11:55:37 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 4AADD585 for ; Sat, 6 Mar 2021 11:55:36 +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: <1615031727.b0ebcbef4027efb671812d1c0d9be250935b3c2b.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/lumpy-sv/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild sci-biology/lumpy-sv/lumpy-sv-9999.ebuild X-VCS-Directories: sci-biology/lumpy-sv/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: b0ebcbef4027efb671812d1c0d9be250935b3c2b X-VCS-Branch: master Date: Sat, 6 Mar 2021 11:55:36 +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: d60b6dd1-6066-4e85-a513-f48c105b932d X-Archives-Hash: 25789520d4a58899cc5bd26b3c276367 commit: b0ebcbef4027efb671812d1c0d9be250935b3c2b Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 11:55:27 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 11:55:27 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0ebcbef sci-biology/lumpy-sv: EAPI bump, fix build Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> ...{lumpy-sv-9999.ebuild => lumpy-sv-0.3.1.ebuild} | 28 ++++++++++------------ 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild similarity index 64% rename from sci-biology/lumpy-sv/lumpy-sv-9999.ebuild rename to sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild index 4c565c0c0..f98892b95 100644 --- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild +++ b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild @@ -1,24 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 - -inherit git-r3 +EAPI=7 DESCRIPTION="Probabilistic framework for structural variant discovery" HOMEPAGE="https://github.com/arq5x/lumpy-sv" -EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git" +SRC_URI="https://github.com/arq5x/lumpy-sv/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="~amd64" -# contains bundled htslib -CDEPEND="dev-util/cmake" -DEPEND="" +DEPEND="sci-libs/htslib" RDEPEND="${DEPEND}" +src_prepare() { + default + # do not build bundled htslib, link to system lib + sed -i -e 's/lumpy_filter: htslib/lumpy_filter:/g' Makefile || die + sed -i -e 's/-I..\/..\/lib\/htslib\///' -e 's/..\/..\/lib\/htslib\/libhts.a/-lhts/g' src/filter/Makefile || die +} + src_install(){ cat > "${T}"/99lumpy-sv <<- EOF LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv @@ -35,9 +37,5 @@ src_install(){ rm scripts/"$f" || die done doins scripts/* - dodoc README.md - insinto /usr/share/lumpy-sv/scripts/bamkit - cd scripts/bamkit || die - doins *.py sectosupp - newdoc README.md README_bamkit.md + einstalldocs }