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, 63 insertions, 0 deletions

diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
new file mode 100644
index 000000000000..5c0e901d9aba
--- /dev/null
+++ b/sci-biology/cutg/Manifest
@@ -0,0 +1 @@
+DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
new file mode 100644
index 000000000000..46163bc2a80f
--- /dev/null
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Codon usage tables calculated from GenBank"
+HOMEPAGE="http://www.kazusa.or.jp/codon/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+	if use emboss; then
+		mkdir CODONS || die
+		ebegin "Indexing CUTG for usage with EMBOSS."
+		EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
+			"Indexing CUTG failed."
+		eend
+	fi
+}
+
+src_install() {
+	local file
+	dodoc README CODON_LABEL SPSUM_LABEL
+	if ! use minimal; then
+		dodir /usr/share/${PN}
+		mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \
+			"Installing raw CUTG database failed."
+	fi
+
+	if use emboss; then
+		dodir /usr/share/EMBOSS/data/CODONS
+		cd CODONS || die
+		for file in *; do
+			mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \
+				"Installing the EMBOSS-indexed database failed."
+		done
+	fi
+}
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
new file mode 100644
index 000000000000..59b110912ca6
--- /dev/null
+++ b/sci-biology/cutg/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <longdescription>
+		Codon usage tables maintained at the Kazusa DNA Research Institute.
+		Codon usage in individual genes has been calculated using the
+		nucleotide sequence data obtained from the GenBank Genetic Sequence
+		Database. The compilation of codon usage is synchronized with each
+		major release of GenBank.
+	</longdescription>
+</pkgmetadata>