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

[Martin Mokrejs]

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 <patrick@g.o> 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@g.o> allpathslg-42337.ebuild,
+  +allpathslg-47093.ebuild:
+  Version Bump
+
+  11 Mar 2013; Justin Lecher <jlec@g.o> metadata.xml:
+  Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+  20 Feb 2013; Justin Lecher <jlec@g.o> -allpathslg-37578.ebuild:
+  Drop old
+
+  20 Feb 2013; Agostino Sarubbo <ago@g.o> allpathslg-42337.ebuild:
+  Stable for amd64, wrt bug #458106
+
+  18 Feb 2013; Justin Lecher <jlec@g.o> -allpathslg-41839.ebuild,
+  metadata.xml:
+  Drop old
+
+  14 Dec 2012; Ulrich Müller <ulm@g.o> allpathslg-37578.ebuild,
+  allpathslg-41839.ebuild, allpathslg-42337.ebuild:
+  Fix LICENSE, MIT (Expat) according to COPYING file.
+
+  19 Nov 2012; Justin Lecher <jlec@g.o> 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@g.o> +allpathslg-42337.ebuild:
+  Version bump, fix compilation errors with gcc-4.7, #425472
+
+*allpathslg-41839 (29 May 2012)
+
+  29 May 2012; Andrey Kislyuk <weaver@g.o> -allpathslg-38573.ebuild,
+  -allpathslg-40063.ebuild, +allpathslg-41839.ebuild:
+  version bump
+
+*allpathslg-40063 (28 Dec 2011)
+
+  28 Dec 2011; Andrey Kislyuk <weaver@g.o>
+  -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild:
+  Version bump, remove old
+
+  15 Oct 2011; Markos Chandras <hwoarang@g.o> allpathslg-37578.ebuild:
+  Stable on amd64 wrt bug #384379
+
+*allpathslg-38573 (25 Sep 2011)
+
+  25 Sep 2011; Andrey Kislyuk <weaver@g.o> +allpathslg-38573.ebuild:
+  Version bump
+
+*allpathslg-37578 (20 Jun 2011)
+
+  20 Jun 2011; Andrey Kislyuk <weaver@g.o> +allpathslg-37578.ebuild:
+  Version bump
+
+*allpathslg-35725-r1 (27 Jan 2011)
+
+  27 Jan 2011; Andrey Kislyuk <weaver@g.o> -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@g.o> +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>