[gentoo-commits] gentoo-x86 commit in sci-biology/tophat: metadata.xml ChangeLog tophat-1.3.2.ebuild

[Andrey Kislyuk (weaver)]

weaver      11/09/26 15:33:22

  Modified:             metadata.xml ChangeLog
  Added:                tophat-1.3.2.ebuild
  Log:
  Version bump
  
  (Portage version: 2.2.0_alpha45/cvs/Linux x86_64)

Revision  Changes    Path
1.2                  sci-biology/tophat/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/metadata.xml?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/metadata.xml?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/metadata.xml?r1=1.1&r2=1.2

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/tophat/metadata.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- metadata.xml	7 Dec 2009 15:50:08 -0000	1.1
+++ metadata.xml	26 Sep 2011 15:33:22 -0000	1.2
@@ -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>



1.5                  sci-biology/tophat/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?r1=1.4&r2=1.5

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- ChangeLog	5 Apr 2010 12:08:12 -0000	1.4
+++ ChangeLog	26 Sep 2011 15:33:22 -0000	1.5
@@ -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@g.o> +tophat-1.3.2.ebuild:
+  Version bump
 
   05 Apr 2010; Pawel Hajdan jr <phajdan.jr@g.o> tophat-1.0.12.ebuild:
   x86 stable wrt bug #311829



1.1                  sci-biology/tophat/tophat-1.3.2.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/tophat-1.3.2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/tophat-1.3.2.ebuild?rev=1.1&content-type=text/plain

Index: tophat-1.3.2.ebuild
===================================================================
# 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
}