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author | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-30 21:36:20 +0200 |
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committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2015-03-30 21:36:20 +0200 |
commit | 1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24 (patch) | |
tree | 98b317cbfd9fa924fa9df2806592586580ddf729 /sci-biology | |
parent | sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 ... (diff) | |
download | sci-1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24.tar.gz sci-1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24.tar.bz2 sci-1b6ab4256d7bcac9f54bac2ed2bb33dbb9183c24.zip |
sci-biology/allpathslg: version bump; added dependency on >=gcc-4.7
Package-Manager: portage-2.2.18
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/allpathslg/ChangeLog | 76 | ||||
-rw-r--r-- | sci-biology/allpathslg/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/allpathslg/allpathslg-52415.ebuild | 39 | ||||
-rw-r--r-- | sci-biology/allpathslg/metadata.xml | 5 |
4 files changed, 121 insertions, 0 deletions
diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog new file mode 100644 index 000000000..5e25459f8 --- /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 <patrick@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 <jlec@gentoo.org> allpathslg-42337.ebuild, + +allpathslg-47093.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-37578.ebuild: + Drop old + + 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> allpathslg-42337.ebuild: + Stable for amd64, wrt bug #458106 + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-41839.ebuild, + metadata.xml: + Drop old + + 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> allpathslg-37578.ebuild, + allpathslg-41839.ebuild, allpathslg-42337.ebuild: + Fix LICENSE, MIT (Expat) according to COPYING file. + + 19 Nov 2012; Justin Lecher <jlec@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 <jlec@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 <weaver@gentoo.org> -allpathslg-38573.ebuild, + -allpathslg-40063.ebuild, +allpathslg-41839.ebuild: + version bump + +*allpathslg-40063 (28 Dec 2011) + + 28 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> + -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild: + Version bump, remove old + + 15 Oct 2011; Markos Chandras <hwoarang@gentoo.org> allpathslg-37578.ebuild: + Stable on amd64 wrt bug #384379 + +*allpathslg-38573 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-38573.ebuild: + Version bump + +*allpathslg-37578 (20 Jun 2011) + + 20 Jun 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-37578.ebuild: + Version bump + +*allpathslg-35725-r1 (27 Jan 2011) + + 27 Jan 2011; Andrey Kislyuk <weaver@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 <weaver@gentoo.org> +allpathslg-35725.ebuild, + +metadata.xml: + Package move from sci-biology/allpaths and version bump diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest new file mode 100644 index 000000000..017e9b530 --- /dev/null +++ b/sci-biology/allpathslg/Manifest @@ -0,0 +1 @@ +DIST allpathslg-52415.tar.gz 3129266 SHA256 3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512 afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6 WHIRLPOOL de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785 diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild new file mode 100644 index 000000000..8750b5f64 --- /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 000000000..f17a827e3 --- /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> |