proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

3 files changed, 65 insertions, 0 deletions

diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
new file mode 100644
index 000000000000..5f4296e01d47
--- /dev/null
+++ b/sci-biology/repeatmasker/Manifest
@@ -0,0 +1 @@
+DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /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>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
new file mode 100644
index 000000000000..acef7d5caf4b
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+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"
+
+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
+}