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

[Martin Mokrejs]

commit:     731ea47715109fabdd7cc3944b6c522509619f56
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Feb 26 08:48:45 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 26 08:49:28 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=731ea477

sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild        |  2 +-
 sci-biology/bowtie/bowtie-2.3.5-r1.ebuild          | 63 ----------------------
 .../{bowtie-2.3.5.1.ebuild => bowtie-2.4.0.ebuild} |  2 +-
 3 files changed, 2 insertions(+), 65 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
index fcf0b4516..f7a1b92d4 100644
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6

diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
deleted file mode 100644
index 2a6fc04eb..000000000
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
-	tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	sys-libs/readline"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch
-	"${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch )
-
-pkg_pretend() {
-	if ! use cpu_flags_x86_sse2 ; then
-		eerror "This package requires a CPU supporting the SSE2 instruction set."
-		die "SSE2 support missing"
-	fi
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CXX="$(tc-getCXX)" \
-		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
-}

diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild b/sci-biology/bowtie/bowtie-2.4.0.ebuild
similarity index 97%
rename from sci-biology/bowtie/bowtie-2.3.5.1.ebuild
rename to sci-biology/bowtie/bowtie-2.4.0.ebuild
index c2fef8667..a4d6837ba 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6