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 704FF139086 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 B1E2F234098; Wed, 11 Jan 2017 23:27:05 +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 7E43F234098 for ; Wed, 11 Jan 2017 23:27:05 +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 91F9D34165B 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 44ADE2435 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: <1484089325.f700625100d351a1ca36b068ac06cc66f90cf7dc.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-1.141.ebuild sci-biology/picard/picard-2.2.2.ebuild sci-biology/picard/picard-2.8.1.ebuild X-VCS-Directories: sci-biology/picard/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f700625100d351a1ca36b068ac06cc66f90cf7dc 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: 7d52185c-ce4d-4fb1-b77c-d9a5c05eb1d4 X-Archives-Hash: b0d75b06c768321a7afd12a5b2884ad9 commit: f700625100d351a1ca36b068ac06cc66f90cf7dc Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jan 10 23:02:05 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jan 10 23:02:05 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7006251 sci-biology/picard: upstream moved from ant to gradle build system Building does not work for me due to: https://github.com/broadinstitute/picard/issues/693 Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/picard/picard-1.141.ebuild | 2 +- sci-biology/picard/picard-2.2.2.ebuild | 2 +- .../{picard-2.2.2.ebuild => picard-2.8.1.ebuild} | 29 +++++++++++++--------- 3 files changed, 19 insertions(+), 14 deletions(-) diff --git a/sci-biology/picard/picard-1.141.ebuild b/sci-biology/picard/picard-1.141.ebuild index ab65edb..b84d91d 100644 --- a/sci-biology/picard/picard-1.141.ebuild +++ b/sci-biology/picard/picard-1.141.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.2.2.ebuild index c43b52c..f0cc489 100644 --- a/sci-biology/picard/picard-2.2.2.ebuild +++ b/sci-biology/picard/picard-2.2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/picard/picard-2.2.2.ebuild b/sci-biology/picard/picard-2.8.1.ebuild similarity index 63% copy from sci-biology/picard/picard-2.2.2.ebuild copy to sci-biology/picard/picard-2.8.1.ebuild index c43b52c..4d09e8d 100644 --- a/sci-biology/picard/picard-2.2.2.ebuild +++ b/sci-biology/picard/picard-2.8.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -16,7 +16,7 @@ SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.t LICENSE="MIT" SLOT="0" IUSE="" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" CDEPEND="dev-java/snappy:1.1 dev-java/cofoja:0 @@ -41,14 +41,19 @@ java_prepare() { epatch "${FILESDIR}"/${PV}-build.xml.patch } -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_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 } + +#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 +#}