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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-31 00:44:17 +0200 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-31 00:44:17 +0200 |
commit | d80145ef93597dea34ba14fb06ee4975740c6c84 (patch) | |
tree | 82bc8b7d98a9202c6dcd978fc436e402a79dd63b | |
parent | renamed to maker (diff) | |
download | sci-d80145ef93597dea34ba14fb06ee4975740c6c84.tar.gz sci-d80145ef93597dea34ba14fb06ee4975740c6c84.tar.bz2 sci-d80145ef93597dea34ba14fb06ee4975740c6c84.zip |
sci-biology/augustus: version bump, new license (temporarily), new dependencies since 3.0 series
Package-Manager: portage-2.2.18
-rw-r--r-- | sci-biology/augustus/ChangeLog | 78 | ||||
-rw-r--r-- | sci-biology/augustus/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/augustus/augustus-3.0.3.ebuild | 59 | ||||
-rw-r--r-- | sci-biology/augustus/metadata.xml | 5 |
4 files changed, 143 insertions, 0 deletions
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog new file mode 100644 index 000000000..ee07f1637 --- /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 <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -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 <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for x86, wrt bug #454842 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for amd64, wrt bug #454842 + +*augustus-2.5.5 (23 Jun 2011) + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> 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 <hwoarang@gentoo.org> augustus-2.4.ebuild: + Stable on amd64 wrt bug #353573 + + 09 Mar 2011; Thomas Kahle <tomka@gentoo.org> augustus-2.4.ebuild: + x86 stable per bug 353573 + + 04 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + augustus-2.5.ebuild: + Respect LDFLAGS + +*augustus-2.5 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + +augustus-2.5.ebuild: + Version bump, update SRC_URI + +*augustus-2.4 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -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 <pacho@gentoo.org> augustus-2.3.1.ebuild: + amd64 stable, bug 298767 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + augustus-2.3.1.ebuild: + stable x86, bug 298767 + +*augustus-2.3.1 (16 Nov 2009) + + 16 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +augustus-2.3.1.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> augustus-2.1.ebuild: + amd64/x86 stable, bug #290924 + + 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> 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 <weaver@gentoo.org> + -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 <weaver@gentoo.org> + +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/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000..1a68ffa25 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1 @@ +DIST augustus-3.0.3.tar.gz 81617475 SHA256 557364b86483c67ee11d05c074e12157ced7e4f4fe779889cd54c2c22579bf2d SHA512 8d573e800551aa8011e5663705b08a3ab4bc04acfb05041dd53738f40c8aec2ecb5794b9173a07f3ff0380413a9b6867f03cd3e7001b704eef2ebcab656452ab WHIRLPOOL d57dff333f0786b19278e971303a13d5d77c5e01d803c8e488505d6c1efa24068a0052ef5f7f9b8d1b5f9e954f0b9b64124a90acdc3896776ef23b01166920e7 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 000000000..da2db427c --- /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 000000000..f17a827e3 --- /dev/null +++ b/sci-biology/augustus/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> |