From b00615d22b9a7f812e10a225b64c241d474958f7 Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <kislyuk@devel.(none)>
Date: Fri, 27 Feb 2009 07:33:00 -0500
Subject: New package sci-biology/bowtie

---
 sci-biology/bowtie/ChangeLog           |  7 +++++++
 sci-biology/bowtie/Manifest            |  3 +++
 sci-biology/bowtie/bowtie-0.9.9.ebuild | 29 +++++++++++++++++++++++++++++
 3 files changed, 39 insertions(+)
 create mode 100644 sci-biology/bowtie/ChangeLog
 create mode 100644 sci-biology/bowtie/Manifest
 create mode 100644 sci-biology/bowtie/bowtie-0.9.9.ebuild

(limited to 'sci-biology/bowtie')

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
new file mode 100644
index 000000000..c5f7214d2
--- /dev/null
+++ b/sci-biology/bowtie/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/bowtie
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  27 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/bowtie, ebuild written by me
+
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
new file mode 100644
index 000000000..7fc7865dc
--- /dev/null
+++ b/sci-biology/bowtie/Manifest
@@ -0,0 +1,3 @@
+DIST bowtie-0.9.9-src.zip 10359925 RMD160 4d8ac96196706156693173e423a47e202b5462f3 SHA1 a4eaaa5efaa63c536baa8858915b610ad5cdfc3e SHA256 762a7420a0f53e1119875bc632db3409180fefed81a2b15240835dd5aaf1e7a7
+EBUILD bowtie-0.9.9.ebuild 790 RMD160 bd113200e595a48c72f4deadfb9581cce22eb94f SHA1 044e028c7be8bdaac555e8b5679f0f4194e1d2fd SHA256 d44715c9eb51334a5e87cbaba1703b89bf9a3af74a1aa5d8dfe795bba111499f
+MISC bowtie-0.9.9.ebuild~ 697 RMD160 e5dc498efb2b0ecc1f40811da42327c3b56c794d SHA1 1de6c878e147e11cbdf9a06647ed14e3acd6a30b SHA256 0352b4b553b3bc1cf6cdceb57d60f1312dee4be3fd325364ecb9a71e61d5014c
diff --git a/sci-biology/bowtie/bowtie-0.9.9.ebuild b/sci-biology/bowtie/bowtie-0.9.9.ebuild
new file mode 100644
index 000000000..7c4f4ab97
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.9.9.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/maq-0.7.1.ebuild,v 1.3 2009/02/26 17:36:19 weaver Exp $
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# FIXME: Requires patching for gcc 4.3
+
+src_unpack() {
+	unpack ${A}
+	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile"
+}
+
+src_install() {
+	dobin bowtie bowtie-* || die
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL
+}
-- 
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