[gentoo-commits] proj/sci:master commit in: sci-biology/augustus/

[Martin Mokrejs]

commit:     d80145ef93597dea34ba14fb06ee4975740c6c84
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 22:44:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 <jlec@g.o> metadata.xml:
+  Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+  31 Jan 2013; Justin Lecher <jlec@g.o> -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@g.o> augustus-2.5.5.ebuild:
+  Stable for x86, wrt bug #454842
+
+  31 Jan 2013; Agostino Sarubbo <ago@g.o> augustus-2.5.5.ebuild:
+  Stable for amd64, wrt bug #454842
+
+*augustus-2.5.5 (23 Jun 2011)
+
+  23 Jun 2011; Justin Lecher <jlec@g.o> 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@g.o> augustus-2.4.ebuild:
+  Stable on amd64 wrt bug #353573
+
+  09 Mar 2011; Thomas Kahle <tomka@g.o> augustus-2.4.ebuild:
+  x86 stable per bug 353573
+
+  04 Feb 2011; Andrey Kislyuk <weaver@g.o> augustus-2.4.ebuild,
+  augustus-2.5.ebuild:
+  Respect LDFLAGS
+
+*augustus-2.5 (03 Feb 2011)
+
+  03 Feb 2011; Andrey Kislyuk <weaver@g.o> 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@g.o> -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@g.o> augustus-2.3.1.ebuild:
+  amd64 stable, bug 298767
+
+  29 Dec 2009; Christian Faulhammer <fauli@g.o>
+  augustus-2.3.1.ebuild:
+  stable x86, bug 298767
+
+*augustus-2.3.1 (16 Nov 2009)
+
+  16 Nov 2009; Andrey Kislyuk <weaver@g.o> +augustus-2.3.1.ebuild:
+  Version bump
+
+  31 Oct 2009; Markus Meier <maekke@g.o> augustus-2.1.ebuild:
+  amd64/x86 stable, bug #290924
+
+  09 Aug 2009; Samuli Suominen <ssuominen@g.o> 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@g.o>
+  -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@g.o>
+  +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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>