Version bump, switch over to sci-biology/rmblast

Package-Manager: portage-2.2_rc86/cvs/Linux x86_64

3 files changed, 69 insertions, 3 deletions

diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index 9292ced2af41..350da2366896 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/repeatmasker
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.4 2009/08/20 13:41:10 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.5 2011/02/03 01:34:28 weaver Exp $
+
+*repeatmasker-3.2.9 (03 Feb 2011)
+
+  03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org>
+  +repeatmasker-3.2.9.ebuild:
+  Version bump, switch over to sci-biology/rmblast
 
 *repeatmasker-3.2.8 (20 Aug 2009)
 
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
index 04817cd71baa..783ffd119e36 100644
--- a/sci-biology/repeatmasker/Manifest
+++ b/sci-biology/repeatmasker/Manifest
@@ -1,6 +1,8 @@
 DIST RepeatMasker-open-3-2-7.tar.gz 11398018 RMD160 63a79ea9146805cc1e7f4cca8b94903136bf2a0c SHA1 22ca2ea2369e1543d58c82954870e114e25c80b9 SHA256 3ceb21658f23780c345d27bb603ef407b953c59dce5b97436a578d28dcb7e477
 DIST RepeatMasker-open-3-2-8.tar.gz 14096137 RMD160 0f8b463bc9d0d8ac71c0d9261ed7161bcaac63f9 SHA1 76684c1fa85049c5c124df718a08d4d21ab684fe SHA256 644c705db9ec239e9a372d0a262548a4a84b58738775f1427021bdbef90a21c1
+DIST RepeatMasker-open-3-2-9.tar.gz 14123559 RMD160 219cb2c2668346d51ddc7c03f63e24064e84968a SHA1 a8df75da847ea64afec2c2f5fcab915d383c7e45 SHA256 60597ac511f2ad37200b80a69c29a4bccfbc7fe697a6400ce19cb6af83dc71d2
 EBUILD repeatmasker-3.2.7.ebuild 1655 RMD160 f36843903117759852420d27c3b75918846df3ff SHA1 a10f55d589c0abf4f106a346623a8565da44752e SHA256 aa304e8c744fb8f875a0804b8b2ca5d492ffb140a100f1bade7e6da42b6c0c09
 EBUILD repeatmasker-3.2.8.ebuild 1655 RMD160 d08c4b1f921bf8026d04af062227c99fbd9c4bc5 SHA1 3995ebad225693aa83f6744ee346555f25c4f950 SHA256 73bc60d01f51809b2bc5ad3186a434b711ccf19bb7fe1a10b73767152873c185
-MISC ChangeLog 1118 RMD160 2e326b82df4fb5ea56bc7056786071025af09cc1 SHA1 f9af350c3d78b9de3e6b80a9cbd0518ca28eecaf SHA256 b5a12a675c2f320127cead80b9bc4b7e40b0c03154f840cb4806654c8ef71f13
+EBUILD repeatmasker-3.2.9.ebuild 1665 RMD160 2eecf7a2e1e08cc91102620c457d54f41d75446f SHA1 d9243084592bdcce6656febee2f4fe1328514d28 SHA256 a7ca538a466a473444f0f9f180760d4317a3f259d653e8608294823883c21e91
+MISC ChangeLog 1285 RMD160 41cc016eda4f3900dc369eb9ea993ea77455cab2 SHA1 05602ae50f63e50b3efae96ecbb1ccf79403fbff SHA256 590374ed56ca5f2d87606fa383e17acb428230b8e3efde4497e8a10cb9d51a47
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild
new file mode 100644
index 000000000000..4b333576eced
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild,v 1.1 2011/02/03 01:34:28 weaver Exp $
+
+EAPI="2"
+
+MY_PV=${PV//\./-}
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="sci-biology/rmblast
+	sci-biology/trf
+	>=sci-biology/repeatmasker-libraries-20090604"
+
+S="${WORKDIR}/RepeatMasker"
+
+src_configure() {
+	sed -i -e 's/system( "clear" );//' \
+		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
+	echo "
+env
+/usr/share/${PN}
+/usr/bin
+2
+/opt/rmblast/bin
+Y
+5" | "${S}/configure" || die "configure failed"
+	sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
+		-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
+		-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
+		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+	exeinto /usr/share/${PN}
+	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
+		doexe $i || die
+		dosym /usr/share/${PN}/$i /usr/bin/$i || die
+	done
+
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins "${S}"/*.pm || die
+
+	insinto /usr/share/${PN}
+	doins -r util Matrices Libraries taxonomy.dat *.help || die
+	keepdir /usr/share/${PN}/Libraries
+
+	dodoc README INSTALL *.help
+}