sci-biology/bowtie: Version bump to 2.2.6

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

3 files changed, 61 insertions, 0 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 42bdbdfd4..6530be026 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/Manifest b/sci-biology/bowtie/Manifest
index 984902e72..dbc0aab6a 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -2,3 +2,4 @@ DIST bowtie-1.1.1-src.zip 7711451 SHA256 92aacb2d32065ebee433ce76eff673c24ed1259
 DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
 DIST bowtie2-2.2.3-source.zip 5724584 SHA256 c4f5ce9f0f53a6b8c7f573a26e96f6909f25bd4e0e8bd77191eaa10671baf0bf SHA512 3baf0e764a79e34b6767a62d52777fc528a82481f417ea5f1b24f38e01fac68c2870daff3060c8da11681d3270e15a10ede034356522336a94f0936d70874684 WHIRLPOOL e19ea1cee85c5ccbc198a981587e8832ebfb4bd9a02332d8171d218e89e6c84df5760db6cd1f8195b712097c6ff3ae7790415d1e63afd2632979392709de26ab
 DIST bowtie2-2.2.5-source.zip 5725798 SHA256 e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 SHA512 8b97860fea73ef36a60dee3dbccdfc956ac7f619ec47a7b820d1df09cff8f77362ddc8071b59ea8021444bda59757d68bdf486fb453d5c4e4b896198bc465d60 WHIRLPOOL 7a8eb7e6d723ccb807a1db3b724326764f8f339017c0b4eb6b234e034458e736ba521106bcc8347c3c428008d8f138f463f3c3e6033b781e1c41898735c2a878
+DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
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 000000000..fce298569
--- /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
+}