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

["Marius Brehler" <marbre@linux.sungazer.de>]

commit:     87642b198308aa88ce351b935b79a58a08cf164b
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sat Oct 10 17:48:48 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Oct 10 17:48:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=87642b19

sci-biology/bowtie: Version bump to 2.2.6

dev-cpp/tbb is now supported with 'tbb' USE flag.

 sci-biology/bowtie/ChangeLog           |  6 ++++
 sci-biology/bowtie/bowtie-2.2.6.ebuild | 54 ++++++++++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 42bdbdf..6530be0 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*bowtie-2.2.6 (10 Oct 2015)
+
+  10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-2.2.6.ebuild:
+  sci-biology/bowtie: Version bump to 2.2.6, support dev-cpp/tbb with
+  USE flag.
+
 *bowtie-1.1.2 (10 Oct 2015)
 
   10 Oct 2015; Ted Tanberry <ted.tanberry@gmail.com> +bowtie-1.1.2.ebuild,

diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild
new file mode 100644
index 0000000..fce2985
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 tbb"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
+		app-arch/unzip
+		tbb? ( dev-cpp/tbb )"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CFLAGS="" \
+		CXXFLAGS="" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS} -msse2" \
+		WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+	dobin ${PN}2 ${PN}2-*
+
+	exeinto /usr/libexec/${PN}2
+	doexe scripts/*
+
+	newman MANUAL ${PN}2.1
+	einstalldocs
+
+	if use examples; then
+		insinto /usr/share/${PN}2
+		doins -r example
+	fi
+}