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

4 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
new file mode 100644
index 000000000000..e8ecdb88e2ea
--- /dev/null
+++ b/sci-biology/bedtools/Manifest
@@ -0,0 +1,2 @@
+DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772
+DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84
diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild
new file mode 100644
index 000000000000..7de4f347c710
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.16.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/BEDTools-Version-${PV}"
+
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+	sed -i \
+		-e '/export CXXFLAGS/ d' \
+		-e '/export CXX/ d' \
+		Makefile || die
+}
+
+src_install() {
+	dobin bin/*
+	dodoc README* RELEASE_HISTORY
+	insinto /usr/share/${PN}
+	doins -r genomes
+}
diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild
new file mode 100644
index 000000000000..cdba954f6d27
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.20.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/bedtools2-${PV}"
+
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+	sed -i \
+		-e '/export CXXFLAGS/ d' \
+		-e '/export CXX/ d' \
+		Makefile || die
+}
+
+src_install() {
+	dobin bin/*
+	dodoc README* RELEASE_HISTORY
+	insinto /usr/share/${PN}
+	doins -r genomes
+}
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
new file mode 100644
index 000000000000..6edffa4a6dc3
--- /dev/null
+++ b/sci-biology/bedtools/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <herd>proxy-maintainers</herd>
+  <maintainer>
+    <email>mmokrejs@gmail.com</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <longdescription>
+    BEDTools: a flexible suite of utilities for comparing genomic features.
+  </longdescription>
+  <upstream>
+    <remote-id type="google-code">bedtools</remote-id>
+    <remote-id type="github">arq5x/bedtools2</remote-id>
+  </upstream>
+</pkgmetadata>