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 6A10A139085 for ; Wed, 11 Jan 2017 23:27:06 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7895F23406B; Wed, 11 Jan 2017 23:27:05 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 44E8C23401C for ; Wed, 11 Jan 2017 23:27:04 +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 5E7C4341659 for ; Wed, 11 Jan 2017 23:27:03 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 89CF2262A for ; Wed, 11 Jan 2017 23:27:01 +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: <1484176959.716ca9a7f85713e713e0f975ed61cbce194a0a67.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/picard/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/picard/picard-2.8.1.ebuild sci-biology/picard/picard-9999.ebuild X-VCS-Directories: sci-biology/picard/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 716ca9a7f85713e713e0f975ed61cbce194a0a67 X-VCS-Branch: master Date: Wed, 11 Jan 2017 23:27:01 +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: b8599a33-e241-42a8-aeca-0f61a1fac3e3 X-Archives-Hash: 93ca6b91f00c8c6731b3f14c1c97d8d0 commit: 716ca9a7f85713e713e0f975ed61cbce194a0a67 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 11 23:22:39 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 11 23:22:39 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=716ca9a7 sci-biology/picard-2.8.1: version bump, do not compile tests by default Also add a live ebuild so we can test upstream with the gradle build system. Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/picard/picard-2.8.1.ebuild | 2 +- .../{picard-2.8.1.ebuild => picard-9999.ebuild} | 29 +++++++++++----------- 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.8.1.ebuild index 4d09e8d..7f8b3fd 100644 --- a/sci-biology/picard/picard-2.8.1.ebuild +++ b/sci-biology/picard/picard-2.8.1.ebuild @@ -44,7 +44,7 @@ java_prepare() { src_compile(){ # work around gradle writing $HOME/.gradle and requiring $HOME/.git # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 - GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die + GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die } #src_install() { diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-9999.ebuild similarity index 68% copy from sci-biology/picard/picard-2.8.1.ebuild copy to sci-biology/picard/picard-9999.ebuild index 4d09e8d..3df5d98 100644 --- a/sci-biology/picard/picard-2.8.1.ebuild +++ b/sci-biology/picard/picard-9999.ebuild @@ -4,14 +4,15 @@ EAPI="6" -JAVA_PKG_IUSE="doc source" +#JAVA_PKG_IUSE="doc source" +JAVA_PKG_IUSE="" -inherit java-pkg-2 java-ant-2 +inherit git-r3 java-pkg-2 java-ant-2 DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files" HOMEPAGE="http://picard.sourceforge.net http://broadinstitute.github.io/picard" -SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz" +EGIT_REPO_URI="https://github.com/broadinstitute/picard.git" LICENSE="MIT" SLOT="0" @@ -44,16 +45,16 @@ java_prepare() { src_compile(){ # work around gradle writing $HOME/.gradle and requiring $HOME/.git # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 - GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die + GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die } -#src_install() { -# cd dist || die -# java-pkg_dojar ${PN}.jar -# java-pkg_dojar ${PN}-lib.jar -# -# java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine -# -# use source && java-pkg_dosrc "${S}"/src/java/* -# use doc && java-pkg_dojavadoc "${S}"/javadoc -#} +src_install() { + cd build/libs || die + java-pkg_dojar "${PN}".jar + java-pkg_dojar "${PN}"-*-SNAPSHOT.jar + + java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine + + #use source && java-pkg_dosrc "${S}"/src/java/* + #use doc && java-pkg_dojavadoc "${S}"/javadoc +}