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Mon, 6 Jan 2014 19:27:07 +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: <1389034965.420e46ff1a1f7709757fae778140fb53c24189d0.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/artemis/ChangeLog sci-biology/artemis/artemis-9999.ebuild sci-biology/artemis/metadata.xml X-VCS-Directories: sci-biology/artemis/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 420e46ff1a1f7709757fae778140fb53c24189d0 X-VCS-Branch: master Date: Mon, 6 Jan 2014 19:27:07 +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: fa59b7a2-b27f-4c4d-bde9-ea9c179da1f9 X-Archives-Hash: 1518981673e9e7bb11b6b9f626bd4809 commit: 420e46ff1a1f7709757fae778140fb53c24189d0 Author: Justin Lecher gentoo org> AuthorDate: Mon Jan 6 19:02:45 2014 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Jan 6 19:02:45 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=420e46ff sci-biology/artemis: Switch from git-2 to git-r3 Package-Manager: portage-2.2.8 --- sci-biology/artemis/ChangeLog | 6 +++++- sci-biology/artemis/artemis-9999.ebuild | 34 ++++++++++----------------------- sci-biology/artemis/metadata.xml | 10 +++++----- 3 files changed, 20 insertions(+), 30 deletions(-) diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog index a992d60..56cbedc 100644 --- a/sci-biology/artemis/ChangeLog +++ b/sci-biology/artemis/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/artemis -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jan 2014; Justin Lecher artemis-9999.ebuild, + metadata.xml: + Switch from git-2 to git-r3 + 07 Feb 2012; Martin Mokrejs artemis-9999.ebuild: sci-biology/artemis: adjust ebuild based on upstream providing a Makefile diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild index 4481975..ca3ddf1 100644 --- a/sci-biology/artemis/artemis-9999.ebuild +++ b/sci-biology/artemis/artemis-9999.ebuild @@ -1,23 +1,15 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 -inherit java-pkg-2 java-ant-2 - -[ "$PV" == "9999" ] && inherit git-2 +inherit java-pkg-2 java-ant-2 git-r3 DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis" - -if [ "$PV" == "9999" ]; then - EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis" - KEYWORDS="~amd64 ~x86" -else - SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz" - KEYWORDS="~amd64 ~x86" -fi +SRC_URI="" +EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis" LICENSE="GPL-2" SLOT="0" @@ -25,19 +17,13 @@ KEYWORDS="" IUSE="" # uses its own BamView -DEPEND="sci-biology/samtools - >=virtual/jdk-1.5 - >=dev-java/sun-jdk-1.5 - dev-java/ant-core" +DEPEND=" + sci-biology/samtools + >=virtual/jdk-1.5 + dev-java/ant-core" RDEPEND="${DEPEND} - >=virtual/jre-1.5" + >=virtual/jre-1.5" # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html # http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial -src_compile() { - emake || die - # ant compile || die - - einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline" -} diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml index 07b5255..2bc8930 100644 --- a/sci-biology/artemis/metadata.xml +++ b/sci-biology/artemis/metadata.xml @@ -1,9 +1,9 @@ - sci-biology - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs +