commit: 60ba53b88755c62f589c3787765bd6f39da78eef
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Fri Feb 6 08:52:03 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 6 20:24:01 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60ba53b8
Updated bowtie:{1,2} ebuilds to match current ebuild policy.
---
sci-biology/bowtie/bowtie-1.1.1.ebuild | 29 +++++++++++++++++++----------
sci-biology/bowtie/bowtie-2.2.4.ebuild | 23 ++++++++++++-----------
2 files changed, 31 insertions(+), 21 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild
b/sci-biology/bowtie/bowtie-1.1.1.ebuild
index ad20591..f152518 100644
--- a/sci-biology/bowtie/bowtie-1.1.1.ebuild
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -4,22 +4,27 @@
EAPI=5
-inherit base eutils toolchain-funcs
+inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/";
-SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
-IUSE=""
KEYWORDS="~amd64 ~x86 ~x64-macos"
+IUSE="examples"
+
DEPEND="app-arch/unzip"
RDEPEND=""
PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+src_prepare() {
+ epatch ${PATCHES[@]}
+}
+
src_compile() {
unset CFLAGS
emake \
@@ -29,14 +34,18 @@ src_compile() {
}
src_install() {
- dobin bowtie bowtie-*
- exeinto /usr/share/${PN}/scripts
- doexe scripts/*
+ dobin ${PN} ${PN}-*
- insinto /usr/share/${PN}
- doins -r genomes indexes
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*
- newman MANUAL bowtie.1
+ newman MANUAL ${PN}
dodoc AUTHORS NEWS TUTORIAL doc/README
- dohtml doc/{manual.html,style.css}
+ docinto html
+ dodoc doc/{manual.html,style.css}
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+ fi
}
diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild
b/sci-biology/bowtie/bowtie-2.2.4.ebuild
index 19e0bca..4b518ca 100644
--- a/sci-biology/bowtie/bowtie-2.2.4.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-inherit base eutils toolchain-funcs
+inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
@@ -12,9 +12,11 @@
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source
LICENSE="GPL-3"
SLOT="2"
-IUSE="examples"
KEYWORDS="~amd64 ~x86"
+IUSE="examples cpu_flags_x86_sse2"
+REQUIRED_USE="cpu_flags_x86_sse2"
+
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
app-arch/unzip"
@@ -23,16 +25,13 @@ S="${WORKDIR}/${PN}2-${PV}"
PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
-pkg_pretend() {
- grep "sse2" /proc/cpuinfo > /dev/null
- if [[ $? -ne 0 ]] ; then
- ewarn "Your processor does not support sse2. Bowtie will
probably not work on this machine."
- fi
+src_prepare() {
+ epatch ${PATCHES[@]}
}
src_compile() {
+ unset CFLAGS
emake \
- CC="$(tc-getCC)" \
CXX="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2"
@@ -40,12 +39,14 @@ src_compile() {
src_install() {
dobin ${PN}2 ${PN}2-*
- exeinto /usr/share/${PN}2/scripts
+
+ exeinto /usr/libexec/${PN}2
doexe scripts/*
- newman MANUAL ${PN}2.1
+ newman MANUAL ${PN}2.2
dodoc AUTHORS NEWS TUTORIAL
- dohtml doc/manual.html doc/style.css
+ docinto html
+ dodoc doc/{manual.html,style.css}
if use examples; then
insinto /usr/share/${PN}2
