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-rw-r--r--sci-biology/bowtie/Manifest4
-rw-r--r--sci-biology/bowtie/bowtie-2.1.0.ebuild56
-rw-r--r--sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch20
-rw-r--r--sci-biology/bowtie/metadata.xml5
4 files changed, 85 insertions, 0 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
new file mode 100644
index 000000000..9321813d2
--- /dev/null
+++ b/sci-biology/bowtie/Manifest
@@ -0,0 +1,4 @@
+AUX bowtie-2.1.0-buildsystem.patch 734 SHA256 8cc4d242c2b61a34503bc5f82a8baaa16c50b743751162060cefb9a3a3234587 SHA512 1d1f61e331874acb9503c4002c45b49f58145b3d7fb0e03245029e88f2783eb0ba01a6b47c1238d7c6fb82e9a3d7e103808f957151d79208b889f4a212d424f8 WHIRLPOOL e53d25c40781cb8eaffbd6990e2da6aaf44f56cf96caea7d89db17db55a48546f5308d682593a24b3a421a97d830dd21c047da9eb82138da29e1a7318319f2ab
+DIST bowtie-2.1.0-source.zip 5697131 SHA256 90a9d3a6bd19ddc3a8f90b935c6a2288478572de2ad4039b29f91016b95ef4b0 SHA512 47535c0539674d81dfac16bf0f0730c766afce93fa91bef7eb4f73df2b73fb7988bc344495a909f81374a60ec79117b141442ff13a61af96fe4043dc0e47cc7c WHIRLPOOL fca873eb10c514c22e2aa46cce685050234c9d2838b7a66c6d5648425b980d93a627c187f26af16e74c6b70e8addb8c267dab5af68023b65591f8ad2616344fa
+EBUILD bowtie-2.1.0.ebuild 1133 SHA256 6a54b6e1b2ac2437fc29bc5e7813312601e176d1786ce607e03e906d54d9ffb5 SHA512 e93d3d51fafb4f39e50a8abf883fa0c6c2df9947a41acf19a69d9cf7432bb411da232545f54925781a7457dec5ca4529bc45a441f188799ec02bc04e66a88f56 WHIRLPOOL cd45fe7e3106861db6e7f0afff34392f13d4c88b2ba7a435f4100e0ad46e13f885514d5c4cf94cbd3d94329bfb4a600314d44b1b2c68bf1955b64ba17a3268f4
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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
+}
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 000000000..97300b1b0
--- /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 000000000..f17a827e3
--- /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>