proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

1 files changed, 52 insertions, 0 deletions

diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
new file mode 100644
index 00000000000..66298cbc197
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	|| (
+		(
+		>=sci-biology/samtools-0.1.18
+		sci-libs/htslib
+		)
+		<sci-biology/samtools-1
+		)
+	>=dev-libs/boost-1.47.0:=
+	<dev-libs/boost-1.56.0:=
+	dev-cpp/eigen:3
+"
+RDEPEND="${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
+}