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authorJustin Lecher <jlec@gentoo.org>2015-03-31 12:52:01 +0200
committerJustin Lecher <jlec@gentoo.org>2015-04-01 08:16:35 +0200
commita9c81628eca87f9cc79d8441dce83f7f0e9d68fd (patch)
tree644f314fc44adcc03cea2a291353526fba42df14
parentsci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc (diff)
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Signed-off-by: Justin Lecher <jlec@gentoo.org>
-rw-r--r--sci-biology/allpathslg/ChangeLog80
-rw-r--r--sci-biology/allpathslg/Manifest1
-rw-r--r--sci-biology/allpathslg/allpathslg-52415.ebuild40
-rw-r--r--sci-biology/allpathslg/metadata.xml5
4 files changed, 0 insertions, 126 deletions
diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog
deleted file mode 100644
index 41ef43838..000000000
--- a/sci-biology/allpathslg/ChangeLog
+++ /dev/null
@@ -1,80 +0,0 @@
-# ChangeLog for sci-biology/allpathslg
-# Copyright 1999-2015 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 $
-
- 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- allpathslg-52415.ebuild:
- sci-biology/allpathslg: noted another home-like web page
-
- 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
deleted file mode 100644
index 017e9b530..000000000
--- a/sci-biology/allpathslg/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index ff7bdcaf2..000000000
--- a/sci-biology/allpathslg/allpathslg-52415.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# 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"
-# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
-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
deleted file mode 100644
index f17a827e3..000000000
--- a/sci-biology/allpathslg/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>