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, 47 insertions, 0 deletions

diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild
new file mode 100644
index 000000000000..04dcc7ce6a25
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.6.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	dev-cpp/sparsehash
+	dev-libs/boost
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	"${FILESDIR}"/${P}-ac_prog_ar.patch
+	)
+
+src_prepare() {
+	tc-export AR
+	sed -i -e "s/-Werror//" configure.ac || die #365195
+	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--docdir="${EPREFIX}/usr/share/doc/${PF}"
+		$(use_enable openmp)
+	)
+	autotools-utils_src_configure
+}