From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 6FEB859CA4 for ; Sun, 14 Feb 2016 17:32:50 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7D36121C003; Sun, 14 Feb 2016 17:32:48 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 8D05821C003 for ; Sun, 14 Feb 2016 17:32:47 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 76914340845 for ; Sun, 14 Feb 2016 17:32:46 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 9FDA610AF for ; Sun, 14 Feb 2016 17:32:44 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1455470236.b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SnpEff/SnpEff-4.1e.ebuild sci-biology/SnpEff/metadata.xml X-VCS-Directories: sci-biology/SnpEff/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd X-VCS-Branch: master Date: Sun, 14 Feb 2016 17:32:44 +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: b4be78c1-2eda-4de4-b322-feca2a7ba5a6 X-Archives-Hash: 60325fb0425b15b41f2a98ad67f5a52d commit: b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd Author: Justin Lecher gentoo org> AuthorDate: Sun Feb 14 17:17:02 2016 +0000 Commit: Justin Lecher gentoo org> CommitDate: Sun Feb 14 17:17:16 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b39edea7 sci-biology/SnpEff: Bump to EAPI=6 * Clean multiverion code Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher gentoo.org> sci-biology/SnpEff/SnpEff-4.1e.ebuild | 48 +++++++++++++++++++---------------- sci-biology/SnpEff/metadata.xml | 2 +- 2 files changed, 27 insertions(+), 23 deletions(-) diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild index 5e9434a..7ba4236 100644 --- a/sci-biology/SnpEff/SnpEff-4.1e.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild @@ -1,51 +1,55 @@ # Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Id$ -EAPI=5 +EAPI=6 inherit java-pkg-2 java-ant-2 -[ "$PV" == "9999" ] && inherit git-2 - DESCRIPTION="Annotate SNP changes and predict their effect" HOMEPAGE="http://snpeff.sourceforge.net" - -if [ "$PV" == "9999" ]; then - EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git" - #EGIT_BRANCH="v4.1B" - KEYWORDS="" -else - SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip - http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" - KEYWORDS="~amd64" - S="${WORKDIR}" -fi +SRC_URI=" + http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip + http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" LICENSE="LGPL-3" SLOT="0" +KEYWORDS="~amd64" IUSE="" # https://github.com/pcingola/SnpEff/blob/master/README_release.txt -DEPEND=">=virtual/jre-1.7:* +DEPEND=" + >=virtual/jre-1.7:* dev-java/maven-bin:* dev-java/antlr:*" RDEPEND="${DEPEND} >=virtual/jdk-1.7:*" + S="${WORKDIR}" + #src_compile(){ # mvn || die #} src_install(){ cd .. || die - mkdir -p "${D}"/usr/share + mkdir -p "${D}"/usr/share || die # but portage does not install the .* files and subdirs, grr! - unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip" - sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die - sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die - sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die - sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + unzip \ + "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share \ + || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip" + sed \ + -e 's#$HOME/tools/picard/#/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/#' \ + -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed \ + -e 's#$HOME/snpEff/#/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#' \ + -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die } # now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/ diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml index 1699e58..f68a1b6 100644 --- a/sci-biology/SnpEff/metadata.xml +++ b/sci-biology/SnpEff/metadata.xml @@ -5,7 +5,7 @@ mmokrejs@fold.natur.cuni.cz Martin Mokrejs - + sci-biology@gentoo.org Gentoo Biology Project