filter as-needed, version bump, fixes bug 401227

Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64

4 files changed, 65 insertions, 10 deletions

diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog
index b6637cee9485..1f97b01cad59 100644
--- a/sci-biology/tophat/ChangeLog
+++ b/sci-biology/tophat/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-biology/tophat
-# 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 $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.6 2012/02/04 23:41:53 weaver Exp $
+
+*tophat-1.4.1 (04 Feb 2012)
+*tophat-1.3.3 (04 Feb 2012)
+
+  04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -tophat-1.3.2.ebuild,
+  +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild:
+  version bump
+
+  04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> tophat-1.3.2.ebuild:
+  filter as-needed
 
 *tophat-1.3.2 (26 Sep 2011)
 
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 667cb922dca8..0f04a0cd1eff 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -2,15 +2,17 @@
 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
+DIST tophat-1.3.3.tar.gz 1404671 RMD160 230deb5ea02200d0a52eef170eddf613173432e8 SHA1 dea6123a428ce1a997068b83e5870e7e0e67ed03 SHA256 f42a51e88a9f9add505ebdef864ede9bf0e58e51eafaf0269171ea7d53f6ce4e
+DIST tophat-1.4.1.tar.gz 1420422 RMD160 45073bcf6c46f621595eae58d61a601dd6fe8d93 SHA1 0513bbcadb7194f12fbddeb3e4033e032f2fb29f SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937
 EBUILD tophat-1.0.12.ebuild 961 RMD160 8017e0f97ebc2e74dee4249551388ae67abf03ff SHA1 e0c6f8c65d42ea8d9a31ad88547a2fecbc96fd3d SHA256 5d96908f1854b5549445f4fb1a6697d604cea465b61e76ba4a8bba4d3ce380fa
-EBUILD tophat-1.3.2.ebuild 679 RMD160 11611f5985a2c7b5aa7637f830b7d0e514b5f055 SHA1 eba3ccd2b405cd67fefd114bd8e002e193b78e90 SHA256 29db179a993ed615f619518f1a4684d4b8033cffe1663083388f874184a19c14
-MISC ChangeLog 848 RMD160 f7026b7779c615cce8b211219f53adf948d287ed SHA1 ca960cd7dca4f40397cd55fa47687bc9d9f66aed SHA256 b7cda8b90e416600f034ee8f1443c686a559b9db5ce14953c3196336f1dfc3bc
+EBUILD tophat-1.3.3.ebuild 752 RMD160 48a65874ca59ee6d08a3e7b7e72cc056a96773c8 SHA1 924ee968e3076c9782c4a9b3934ac46476dfec5d SHA256 d2faface12f50f63e08a961de8f22c70a49f2c94103a0e8f49edab74bb79db37
+EBUILD tophat-1.4.1.ebuild 775 RMD160 ce0041505839aecf26adc891fd5c9b63311afb4c SHA1 db2201ddfcdd06a88fac0666f351b61ea79b3167 SHA256 4669936f5681cc141eda9f50bbd54e0c91582a6b5970271ce5fa23f86e15e497
+MISC ChangeLog 1130 RMD160 5f5eddccf3c8f21a6eb5737c51e4061338bcc468 SHA1 998d8d9e5ce8b5f342e9be393a7d4113f06bef2f SHA256 de582972be0f22fda992f2283753a19bdbab22973995ba329c6977989c97c1e6
 MISC metadata.xml 335 RMD160 b22dd3122da8bf158936a405342e180ca6ae90e7 SHA1 5b45fd576038bb88399efb595c1866f274b372e4 SHA256 ba5318e09c3e0b3d36ac6e6d946da192f0b8dabb80298d5c0e7f8f879c3bcdc0
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-=wIdN
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diff --git a/sci-biology/tophat/tophat-1.3.2.ebuild b/sci-biology/tophat/tophat-1.3.3.ebuild
index ad53ba9f2233..8c1f181f35f9 100644
--- a/sci-biology/tophat/tophat-1.3.2.ebuild
+++ b/sci-biology/tophat/tophat-1.3.3.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.3.3.ebuild,v 1.1 2012/02/04 23:41:53 weaver Exp $
 
 EAPI=4
 
+inherit flag-o-matic
+
 DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
 HOMEPAGE="http://tophat.cbcb.umd.edu/"
 SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
@@ -19,6 +21,10 @@ RDEPEND="${DEPEND}
 
 MAKEOPTS="${MAKEOPTS} -j1"
 
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+}
+
 src_configure() {
 	econf \
 		$(use_with bam) || die
diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild
new file mode 100644
index 000000000000..af728afc0fdf
--- /dev/null
+++ b/sci-biology/tophat/tophat-1.4.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.4.1.ebuild,v 1.1 2012/02/04 23:41:54 weaver Exp $
+
+EAPI=4
+
+inherit flag-o-matic autotools
+
+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_prepare() {
+	filter-ldflags -Wl,--as-needed
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_with bam) || die
+}
+
+src_install() {
+	einstall || die
+	dodoc AUTHORS NEWS THANKS
+}