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Diffstat (limited to 'sci-biology/bowtie/bowtie-2.1.0.ebuild')
-rw-r--r--sci-biology/bowtie/bowtie-2.1.0.ebuild56
1 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
new file mode 100644
index 000000000..26bf770ca
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+IUSE="examples"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
+ app-arch/unzip"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+pkg_pretend() {
+ grep "sse2" /proc/cpuinfo > /dev/null
+ if [[ $? -ne 0 ]] ; then
+ ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine."
+ fi
+}
+
+src_prepare() {
+ epatch "${FILESDIR}/${P}-buildsystem.patch"
+}
+
+src_compile() {
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+ dobin bowtie2 bowtie2-*
+ exeinto /usr/share/${PN}2/scripts
+ doexe scripts/*
+
+ newman MANUAL bowtie2.1
+ dodoc AUTHORS NEWS TUTORIAL
+ dohtml doc/manual.html doc/style.css
+
+ if use examples; then
+ insinto /usr/share/${PN}2
+ doins -r example
+ fi
+}