commit: 1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Mar 30 19:36:20 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Mar 30 19:36:20 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b6ab425
sci-biology/allpathslg: version bump; added dependency on >=gcc-4.7 Package-Manager: portage-2.2.18 sci-biology/allpathslg/ChangeLog | 76 ++++++++++++++++++++++++++ sci-biology/allpathslg/allpathslg-52415.ebuild | 39 +++++++++++++ sci-biology/allpathslg/metadata.xml | 5 ++ 3 files changed, 120 insertions(+) diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog new file mode 100644 index 0000000..5e25459 --- /dev/null +++ b/sci-biology/allpathslg/ChangeLog @@ -0,0 +1,76 @@ +# ChangeLog for sci-biology/allpathslg +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.16 2013/11/13 02:34:46 patrick Exp $ + + 13 Nov 2013; Patrick Lauer <patr...@gentoo.org> allpathslg-42337.ebuild, + allpathslg-47093.ebuild: + Removing x86 keyword as dependency sci-biology/vaal does not work on x86 + +*allpathslg-47093 (17 Jul 2013) + + 17 Jul 2013; Justin Lecher <j...@gentoo.org> allpathslg-42337.ebuild, + +allpathslg-47093.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <j...@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Feb 2013; Justin Lecher <j...@gentoo.org> -allpathslg-37578.ebuild: + Drop old + + 20 Feb 2013; Agostino Sarubbo <a...@gentoo.org> allpathslg-42337.ebuild: + Stable for amd64, wrt bug #458106 + + 18 Feb 2013; Justin Lecher <j...@gentoo.org> -allpathslg-41839.ebuild, + metadata.xml: + Drop old + + 14 Dec 2012; Ulrich Müller <u...@gentoo.org> allpathslg-37578.ebuild, + allpathslg-41839.ebuild, allpathslg-42337.ebuild: + Fix LICENSE, MIT (Expat) according to COPYING file. + + 19 Nov 2012; Justin Lecher <j...@gentoo.org> allpathslg-37578.ebuild, + allpathslg-41839.ebuild, allpathslg-42337.ebuild: + Block sci-biology/allpaths due to file collision, #443740 + +*allpathslg-42337 (09 Jul 2012) + + 09 Jul 2012; Justin Lecher <j...@gentoo.org> +allpathslg-42337.ebuild: + Version bump, fix compilation errors with gcc-4.7, #425472 + +*allpathslg-41839 (29 May 2012) + + 29 May 2012; Andrey Kislyuk <wea...@gentoo.org> -allpathslg-38573.ebuild, + -allpathslg-40063.ebuild, +allpathslg-41839.ebuild: + version bump + +*allpathslg-40063 (28 Dec 2011) + + 28 Dec 2011; Andrey Kislyuk <wea...@gentoo.org> + -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild: + Version bump, remove old + + 15 Oct 2011; Markos Chandras <hwoar...@gentoo.org> allpathslg-37578.ebuild: + Stable on amd64 wrt bug #384379 + +*allpathslg-38573 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <wea...@gentoo.org> +allpathslg-38573.ebuild: + Version bump + +*allpathslg-37578 (20 Jun 2011) + + 20 Jun 2011; Andrey Kislyuk <wea...@gentoo.org> +allpathslg-37578.ebuild: + Version bump + +*allpathslg-35725-r1 (27 Jan 2011) + + 27 Jan 2011; Andrey Kislyuk <wea...@gentoo.org> -allpathslg-35725.ebuild, + +allpathslg-35725-r1.ebuild: + Drop ~x86, avoid collision with sci-biology/vaal + +*allpathslg-35725 (25 Jan 2011) + + 25 Jan 2011; Andrey Kislyuk <wea...@gentoo.org> +allpathslg-35725.ebuild, + +metadata.xml: + Package move from sci-biology/allpaths and version bump diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild new file mode 100644 index 0000000..8750b5f --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-52415.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/allpathslg-42337.ebuild,v 1.6 2013/11/13 02:34:46 patrick Exp $ + +EAPI=4 + +inherit autotools flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"; +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"; + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +# as of release 44849, GCC 4.7.0 (or higher) is required +# seems pre gcc-4.7 users must stay with: +# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz +DEPEND=" + >=sys-devel/gcc-4.7 + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + sed -i 's/-ggdb3//' configure.ac || die + eautoreconf +} + +src_install() { + einstall || die + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${D}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/allpathslg/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>
