From bfc34ae6c9ab746e707af4b2f61d365b1316fc5a Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Mon, 26 Sep 2011 15:33:22 +0000
Subject: [PATCH] Version bump

Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64
---
 sci-biology/tophat/ChangeLog           |  9 ++++++--
 sci-biology/tophat/Manifest            | 16 ++++++++++++--
 sci-biology/tophat/metadata.xml        |  3 +++
 sci-biology/tophat/tophat-1.3.2.ebuild | 30 ++++++++++++++++++++++++++
 4 files changed, 54 insertions(+), 4 deletions(-)
 create mode 100644 sci-biology/tophat/tophat-1.3.2.ebuild

diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index 8eca0dac623a..b6637cee9485 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/tophat
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.4 2010/04/05 12:08:12 phajdan.jr Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.5 2011/09/26 15:33:22 weaver Exp $
+
+*tophat-1.3.2 (26 Sep 2011)
+
+  26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +tophat-1.3.2.ebuild:
+  Version bump
 
   05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> tophat-1.0.12.ebuild:
   x86 stable wrt bug #311829
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index f333737ff28c..667cb922dca8 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,4 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST tophat-1.0.12.tar.gz 468781 RMD160 b705ca7bde20bd143ba1cfd084b3a3e2815a7a4d SHA1 8a39af78dc9ec797f9f30853fb24b6b0e42d0ef6 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2
+DIST tophat-1.3.2.tar.gz 1380873 RMD160 a9f5b6c524fd35922b7952db8830b906cb9b1a9f SHA1 418e9c23e627aedfb6f1888f395c02c961227aab SHA256 0832648c2e9fc09ba42dabd78930be2033820f276c77f2cf578f9b09d2b753f3
 EBUILD tophat-1.0.12.ebuild 961 RMD160 8017e0f97ebc2e74dee4249551388ae67abf03ff SHA1 e0c6f8c65d42ea8d9a31ad88547a2fecbc96fd3d SHA256 5d96908f1854b5549445f4fb1a6697d604cea465b61e76ba4a8bba4d3ce380fa
-MISC ChangeLog 735 RMD160 647bf081768eae10bee2194cc5c38ac6bc228baa SHA1 3c2109f467f5109f64716a2c47093a4f969d7af4 SHA256 2356ee7722704187e2e6cb744b548f444c3ebd09115eaf6776badb6af0cb7f6d
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+EBUILD tophat-1.3.2.ebuild 679 RMD160 11611f5985a2c7b5aa7637f830b7d0e514b5f055 SHA1 eba3ccd2b405cd67fefd114bd8e002e193b78e90 SHA256 29db179a993ed615f619518f1a4684d4b8033cffe1663083388f874184a19c14
+MISC ChangeLog 848 RMD160 f7026b7779c615cce8b211219f53adf948d287ed SHA1 ca960cd7dca4f40397cd55fa47687bc9d9f66aed SHA256 b7cda8b90e416600f034ee8f1443c686a559b9db5ce14953c3196336f1dfc3bc
+MISC metadata.xml 335 RMD160 b22dd3122da8bf158936a405342e180ca6ae90e7 SHA1 5b45fd576038bb88399efb595c1866f274b372e4 SHA256 ba5318e09c3e0b3d36ac6e6d946da192f0b8dabb80298d5c0e7f8f879c3bcdc0
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.11 (GNU/Linux)
+
+iEYEARECAAYFAk6Am0cACgkQ8xSwyhbn2Ob8cgCgn6UGLslGEMmzawQ4x6OLs/9f
+rtwAnjCFf5B8SwKCivtTlhgn8Q+WnupR
+=wIdN
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
index 3302123e5718..6631e9455420 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<use>
+		<flag name='bam'>Compile support for the BAM format</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-biology/tophat/tophat-1.3.2.ebuild b/sci-biology/tophat/tophat-1.3.2.ebuild
new file mode 100644
index 000000000000..ad53ba9f2233
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.3.2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.3.2.ebuild,v 1.1 2011/09/26 15:33:22 weaver Exp $
+
+EAPI=4
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="+bam"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+	sci-biology/bowtie"
+
+MAKEOPTS="${MAKEOPTS} -j1"
+
+src_configure() {
+	econf \
+		$(use_with bam) || die
+}
+
+src_install() {
+	einstall || die
+	dodoc AUTHORS NEWS THANKS
+}
-- 
2.26.2