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
