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

["Christoph Junghans" <ottxor@gentoo.org>]

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