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

[David Seifert]

commit:     20633430c439732edc1dd09d5b76acefcaa54c9d
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug  1 16:40:40 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug  1 16:40:40 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20633430

sci-biology/bowtie: add 2.4.4

Bug: https://bugs.gentoo.org/722870
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/bowtie/Manifest            |  1 +
 sci-biology/bowtie/bowtie-2.4.4.ebuild | 55 ++++++++++++++++++++++++++++++++++
 2 files changed, 56 insertions(+)

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 50ad9715e98..96d35e2bfd2 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1 +1,2 @@
 DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
+DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da

diff --git a/sci-biology/bowtie/bowtie-2.4.4.ebuild b/sci-biology/bowtie/bowtie-2.4.4.ebuild
new file mode 100644
index 00000000000..6621b5babd9
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.4.4.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+S="${WORKDIR}/${PN}2-${PV}"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse2 examples"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/perl
+	sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		CXXFLAGS="" \
+		CPPFLAGS="${CPPFLAGS}" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+	dobin bowtie2 bowtie2-*
+
+	exeinto /usr/libexec/bowtie2
+	doexe scripts/*
+
+	HTML_DOCS=( doc/{manual.html,style.css} )
+	einstalldocs
+	dodoc TUTORIAL
+	newman MANUAL bowtie2.1
+
+	python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
+
+	if use examples; then
+		docinto examples
+		dodoc -r example/.
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}