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Mon, 30 Mar 2015 22:44:42 +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: <1427755457.d80145ef93597dea34ba14fb06ee4975740c6c84.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/augustus/ChangeLog sci-biology/augustus/augustus-3.0.3.ebuild sci-biology/augustus/metadata.xml X-VCS-Directories: sci-biology/augustus/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: d80145ef93597dea34ba14fb06ee4975740c6c84 X-VCS-Branch: master Date: Mon, 30 Mar 2015 22:44:42 +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: 05df8d19-c15e-4503-9582-79f1a43ef638 X-Archives-Hash: 1b0d4a0f3616142760cc2e2bef0c4dd4 commit: d80145ef93597dea34ba14fb06ee4975740c6c84 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Mar 30 22:44:17 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 30 22:44:17 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d80145ef sci-biology/augustus: version bump, new license (temporarily), new dependencies since 3.0 series Package-Manager: portage-2.2.18 sci-biology/augustus/ChangeLog | 78 ++++++++++++++++++++++++++++++ sci-biology/augustus/augustus-3.0.3.ebuild | 59 ++++++++++++++++++++++ sci-biology/augustus/metadata.xml | 5 ++ 3 files changed, 142 insertions(+) diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog new file mode 100644 index 0000000..ee07f16 --- /dev/null +++ b/sci-biology/augustus/ChangeLog @@ -0,0 +1,78 @@ +# ChangeLog for sci-biology/augustus +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $ + + 11 Mar 2013; Justin Lecher metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Jan 2013; Justin Lecher -augustus-2.3.1.ebuild, + -augustus-2.4.ebuild, -augustus-2.5.ebuild, metadata.xml: + Drop old, fixes multiple QA issues, #454822 + + 31 Jan 2013; Agostino Sarubbo augustus-2.5.5.ebuild: + Stable for x86, wrt bug #454842 + + 31 Jan 2013; Agostino Sarubbo augustus-2.5.5.ebuild: + Stable for amd64, wrt bug #454842 + +*augustus-2.5.5 (23 Jun 2011) + + 23 Jun 2011; Justin Lecher augustus-2.3.1.ebuild, + augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild, + +files/augustus-2.5.5-sane-build.patch: + Version Bump, respect LDFLAGS, #337655 + + 09 Mar 2011; Markos Chandras augustus-2.4.ebuild: + Stable on amd64 wrt bug #353573 + + 09 Mar 2011; Thomas Kahle augustus-2.4.ebuild: + x86 stable per bug 353573 + + 04 Feb 2011; Andrey Kislyuk augustus-2.4.ebuild, + augustus-2.5.ebuild: + Respect LDFLAGS + +*augustus-2.5 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk augustus-2.4.ebuild, + +augustus-2.5.ebuild: + Version bump, update SRC_URI + +*augustus-2.4 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk -augustus-2.1.ebuild, + -files/augustus-2.1-glibc-2.10.patch, +augustus-2.4.ebuild: + Version bump, drop old + + 09 Feb 2010; Pacho Ramos augustus-2.3.1.ebuild: + amd64 stable, bug 298767 + + 29 Dec 2009; Christian Faulhammer + augustus-2.3.1.ebuild: + stable x86, bug 298767 + +*augustus-2.3.1 (16 Nov 2009) + + 16 Nov 2009; Andrey Kislyuk +augustus-2.3.1.ebuild: + Version bump + + 31 Oct 2009; Markus Meier augustus-2.1.ebuild: + amd64/x86 stable, bug #290924 + + 09 Aug 2009; Samuli Suominen augustus-2.1.ebuild, + +files/augustus-2.1-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #276719. + +*augustus-2.1 (19 Mar 2009) + + 19 Mar 2009; Andrey Kislyuk + -files/augustus-2.0.3-cflags.patch, -files/augustus-2.0.3-gcc4.3.patch, + -augustus-2.0.3.ebuild, +augustus-2.1.ebuild: + Version bump + +*augustus-2.0.3 (04 Jan 2009) + + 04 Jan 2009; weaver + +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch, + +metadata.xml, +augustus-2.0.3.ebuild: + Initial commit, ebuild written by me diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.0.3.ebuild new file mode 100644 index 0000000..da2db42 --- /dev/null +++ b/sci-biology/augustus/augustus-3.0.3.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.5.ebuild,v 1.3 2013/01/31 18:42:11 ago Exp $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz" + +LICENSE="GPL-3" +# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT +# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT +# LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +DEPEND=" + sci-libs/gsl + dev-libs/boost + sys-libs/zlib + sys-devel/flex" +RDEPEND="${DEPEND}" + +src_prepare() { + # TODO: do we need anything from the 2.5.5 patch? + # epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/augustus/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +