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

[Nicolas Bock]

commit:     a504fdf4dfc52876baaa84103a3f6727a3419ec6
Author:     cel <cel.gentoo <AT> gmail <DOT> com>
AuthorDate: Wed Sep 25 21:55:16 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Sep 25 21:55:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a504fdf4

sci-biology/bowtie: Added ebuild for bowtie-2.1.0.

---
 sci-biology/bowtie/bowtie-2.1.0.ebuild             | 61 ++++++++++++++++++++++
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    | 20 +++++++
 sci-biology/bowtie/metadata.xml                    |  5 ++
 3 files changed, 86 insertions(+)

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 0000000..c2c5024
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+IUSE="sse2 examples"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-lang/perl"
+DEPEND="${CDEPEND} \
+		app-arch/unzip"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+pkg_pretend() {
+	if ! use sse2 ; then
+		ebegin
+		eerror "bowtie2 requires sse2 support. Please make sure your system supports"
+		eerror "sse2 and enable the sse2 use flag."
+		eend
+		die
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-buildsystem.patch"
+}
+
+src_compile() {
+	use sse2 && append-cxxflags -msse2
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+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
+}

diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
new file mode 100644
index 0000000..97300b1
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
@@ -0,0 +1,20 @@
+--- Makefile.old	2013-09-22 12:07:12.606844000 +0200
++++ Makefile	2013-09-22 13:06:03.113888200 +0200
+@@ -24,8 +24,6 @@
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+ CXX = $(CPP)
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+@@ -141,7 +139,7 @@
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  = $(CXXFLAGS)
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE

diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/bowtie/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>