sci-biology/bowtie: version bump, SLOT major version

sci-biology/bowtie is now SLOTed, in order to allow for a
parallel installation with bowtie2. In addition, the latest
bowtie now supports dev-cpp/tbb with 'tbb' USE flag.

1 files changed, 58 insertions, 0 deletions

diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild
new file mode 100644
index 000000000000..55eec5060787
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+IUSE="examples tbb"
+
+DEPEND="app-arch/unzip
+	tbb? ( dev-cpp/tbb )"
+RDEPEND=""
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_prepare() {
+	# Suppress useless -Wall pollution
+	sed -i 's/\-Wall/\-Wno-enum-compare/g' Makefile || die
+
+	# always include tinythread.cpp
+	epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}" \
+		WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+	dobin ${PN} ${PN}-*
+
+	exeinto /usr/libexec/${PN}
+	doexe scripts/*
+
+	newman MANUAL ${PN}.1
+	einstalldocs
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r genomes indexes
+	fi
+}