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, 68 insertions, 0 deletions

diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
new file mode 100644
index 000000000000..affcfb9f045f
--- /dev/null
+++ b/sci-biology/gibbs/Manifest
@@ -0,0 +1 @@
+DIST gibbs-3.1.tar.gz 563300 RMD160 063de85a7f1a62bcd63c0838db62cb344ff27abd SHA1 9e6fcddd6036ea0c19259820dcfffa9286cd4e1f SHA256 e8bd62b7d2580b00fc0cdf32ed75ac1ffac29747c75227269a75fd587ba77b69
diff --git a/sci-biology/gibbs/files/gibbs-demo b/sci-biology/gibbs/files/gibbs-demo
new file mode 100644
index 000000000000..c58ae3b88e04
--- /dev/null
+++ b/sci-biology/gibbs/files/gibbs-demo
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+gibbs /usr/share/gibbs/examples/porins.b185 11 100 -R2000 -s230
+gibbs /usr/share/gibbs/examples/iomps.b58 11 125 -s1
+gibbs /usr/share/gibbs/examples/Igfold.b60x 12,12,12 90,90,90 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 12 150 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 18,18,18 20,20,20 -s1
diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
new file mode 100644
index 000000000000..9ed11b435129
--- /dev/null
+++ b/sci-biology/gibbs/gibbs-3.1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils multilib
+
+DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
+HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
+SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="mpi"
+KEYWORDS="amd64 x86"
+
+DEPEND="
+	mpi? (
+		virtual/mpi
+		sys-cluster/mpe2 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	sed \
+		-e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \
+		-e 's/-Werror//' \
+		-i configure.in || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	if use mpi; then export CC=mpicc; fi
+	local myeconfargs=( $(use_enable mpi) )
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+	exeinto /usr/$(get_libdir)/${PN}
+	doexe *.pl
+	dodoc README ChangeLog
+}
+
+pkg_postinst() {
+	einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}."
+	einfo "These scripts require installation of sci-biology/bioperl."
+}
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
new file mode 100644
index 000000000000..c31e2db70216
--- /dev/null
+++ b/sci-biology/gibbs/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		The Gibbs motif sampler stochastically examines candidate alignments
+		in an effort to find the best alignment as measured by the maximum
+		a posteriori (MAP) log-likelihood ratio.
+	</longdescription>
+</pkgmetadata>