From 2a6b6e68512ffd07ea418cad24a19535a7283906 Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Fri, 27 Feb 2009 00:16:15 +0000
Subject: Import from Science overlay, bug 114096 (Portage version:
 2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64)

---
 sci-biology/repeatmasker/ChangeLog                 | 24 ++++++++++
 sci-biology/repeatmasker/metadata.xml              |  5 ++
 sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild | 54 ++++++++++++++++++++++
 3 files changed, 83 insertions(+)
 create mode 100644 sci-biology/repeatmasker/ChangeLog
 create mode 100644 sci-biology/repeatmasker/metadata.xml
 create mode 100644 sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild

(limited to 'sci-biology/repeatmasker')

diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
new file mode 100644
index 000000000000..96d54c647caf
--- /dev/null
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -0,0 +1,24 @@
+# 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 1.1 2009/02/27 00:16:15 weaver Exp $
+
+*repeatmasker-3.2.7 (26 Feb 2009)
+
+  26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +repeatmasker-3.2.7.ebuild:
+  Import from Science overlay, bug 114096
+
+  19 Feb 2009; weaver <weaver@gentoo.org> ChangeLog:
+  Version bump
+
+  08 Jul 2008; weaver <weaver@gentoo.org> +repeatmasker-3.2.5.ebuild:
+  Version bump
+
+  27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx>
+  +repeatmasker-3.1.7.ebuild:
+  Mass import from sunrise
+
+  20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +repeatmasker-3.1.7.ebuild,
+  +metadata.xml:
+  new package (bug 114096)
+
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 000000000000..7e3286984488
--- /dev/null
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild
new file mode 100644
index 000000000000..5f30e00e0c23
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild,v 1.1 2009/02/27 00:16:15 weaver Exp $
+
+inherit versionator
+
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
+HOMEPAGE="http://repeatmasker.org/"
+SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
+
+LICENSE="OSL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="sci-biology/phrap
+	sci-biology/trf
+	>=sci-biology/repeatmasker-libraries-20090120"
+
+S="${WORKDIR}/RepeatMasker"
+
+src_compile() {
+	sed -i -e 's/system( "clear" );//' \
+		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
+	echo "
+env
+/usr/share/${PN}
+/usr/bin
+1
+/usr/bin
+Y
+4" | "${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}'|' \
+		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
+}
+
+src_install() {
+	dobin DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask
+
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins "${S}"/*.pm
+
+	insinto /usr/share/${PN}
+	doins -r util Matrices Libraries taxonomy.dat
+	keepdir /usr/share/${PN}/Libraries
+
+	dodoc README INSTALL *.help
+}
-- 
cgit v1.2.3-65-gdbad