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 439FC1395E2 for ; Wed, 7 Dec 2016 10:15:15 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9012DE0D79; Wed, 7 Dec 2016 10:15:14 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 6E692E0D79 for ; Wed, 7 Dec 2016 10:15:13 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 18FC034105A for ; Wed, 7 Dec 2016 10:15:13 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 8658724B6 for ; Wed, 7 Dec 2016 10:15:11 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1481105698.5fb831e8c3bcf4b192b96dcf018a558a86bd1581.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SnpEff/SnpEff-4.3g.ebuild X-VCS-Directories: sci-biology/SnpEff/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 5fb831e8c3bcf4b192b96dcf018a558a86bd1581 X-VCS-Branch: master Date: Wed, 7 Dec 2016 10:15:11 +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: 47dcc3b5-b66f-4447-a716-e201de93938f X-Archives-Hash: 64f8ecd5c3d83d5418589ddad7bec9de commit: 5fb831e8c3bcf4b192b96dcf018a558a86bd1581 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Dec 7 10:14:58 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Dec 7 10:14:58 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5fb831e8 sci-biology/SnpEff: fix installation on PREFIX Package-Manager: portage-2.3.2 sci-biology/SnpEff/SnpEff-4.3g.ebuild | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/sci-biology/SnpEff/SnpEff-4.3g.ebuild b/sci-biology/SnpEff/SnpEff-4.3g.ebuild index f817588..fb11894 100644 --- a/sci-biology/SnpEff/SnpEff-4.3g.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3g.ebuild @@ -36,22 +36,22 @@ S="${WORKDIR}" src_install(){ cd .. || die - mkdir -p "${D}"/usr/share || die + mkdir -p "${ED}"/usr/share || die # but portage does not install the .* files and subdirs, grr! unzip \ - "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${D}"/usr/share \ + "${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \ || die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip" sed \ - -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \ + -e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die sed \ - -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' \ + -e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die sed \ - -e 's#$HOME/snpEff/#/usr/share/snpEff/#' \ + -e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die sed \ - -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' \ + -e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \ -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die }