[gentoo-commits] gentoo-x86 commit in sci-biology/cufflinks: ChangeLog cufflinks-2.2.1-r1.ebuild

[Justin Lecher (jlec)]

jlec        14/10/02 08:01:05

  Modified:             ChangeLog
  Added:                cufflinks-2.2.1-r1.ebuild
  Log:
  sci-biology/cufflinks: Drop debugging flags, fix compatibility with newer samtools, #524252
  
  (Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

Revision  Changes    Path
1.9                  sci-biology/cufflinks/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/ChangeLog?rev=1.9&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/ChangeLog?rev=1.9&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/ChangeLog?r1=1.8&r2=1.9

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- ChangeLog	25 Sep 2014 16:11:26 -0000	1.8
+++ ChangeLog	2 Oct 2014 08:01:05 -0000	1.9
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/cufflinks
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.8 2014/09/25 16:11:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.9 2014/10/02 08:01:05 jlec Exp $
+
+*cufflinks-2.2.1-r1 (02 Oct 2014)
+
+  02 Oct 2014; Justin Lecher <jlec@g.o> +cufflinks-2.2.1-r1.ebuild,
+  +files/cufflinks-2.2.1-flags.patch, +files/cufflinks-2.2.1-hts.patch:
+  Drop debugging flags, fix compatibility with newer samtools, #524252
 
 *cufflinks-2.2.1 (25 Sep 2014)
 



1.1                  sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild?rev=1.1&content-type=text/plain

Index: cufflinks-2.2.1-r1.ebuild
===================================================================
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild,v 1.1 2014/10/02 08:01:05 jlec Exp $

EAPI=5

AUTOTOOLS_AUTORECONF=true

inherit autotools-utils flag-o-matic toolchain-funcs

DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"

SLOT="0"
LICENSE="Artistic"
IUSE="debug"
KEYWORDS="~amd64 ~x86"

DEPEND="
	|| (
		(
		>=sci-biology/samtools-0.1.18
		sci-libs/htslib
		)
		<sci-biology/samtools-1
		)
	>=dev-libs/boost-1.47.0:=
	dev-cpp/eigen:3
"
RDEPEND="${DEPEND}"

PATCHES=(
	"${FILESDIR}"/${P}-hts.patch
	"${FILESDIR}"/${P}-flags.patch
	)

src_prepare() {
	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
	autotools-utils_src_prepare
}

src_configure() {
	local myeconfargs=(
		--disable-optim
		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
		--with-bam="${EPREFIX}/usr/"
		$(use_enable debug)
	)
	autotools-utils_src_configure
}