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, 51 insertions, 0 deletions

diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
new file mode 100644
index 000000000000..e17b1c93e220
--- /dev/null
+++ b/sci-biology/uchime/Manifest
@@ -0,0 +1 @@
+DIST uchime4.2.40_src.tar.gz 66772 SHA256 cb6a3aea4e8b4343a6e0ddde3b2755bbec53492bae5d6252ce8a7091061f353d SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b WHIRLPOOL 28ad19892ac8b4db03e93fd1fca39b05d6675c241a97f7a2ab241765589b34c56684ab4923eaf568a5f9b0e1583ce1460be7f0edf9d9201e5d3db3da0efb0ee6
diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt
new file mode 100644
index 000000000000..54b0a3ba0d30
--- /dev/null
+++ b/sci-biology/uchime/files/CMakeLists.txt
@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 2.6)
+project(UCHIME)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
+
+# Simply copy the source files from the mk script
+add_executable(uchime 
+				addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp)
+
+INSTALL(TARGETS uchime
+        DESTINATION bin)
diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml
new file mode 100644
index 000000000000..a3c0f91c8a08
--- /dev/null
+++ b/sci-biology/uchime/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+UCHIME is a new algorithm for detecting chimeric sequences. It was developed in 
+collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob 
+Knight. Chimeras are commonly created during DNA sample amplification by 
+PCR, especially in community sequencing experiments using single regions 
+such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can 
+detect chimeras using a reference database or de novo using abundance 
+information on the assumption that chimeras are less abundant than their 
+parents because they must have undergone fewer rounds of amplification.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild
new file mode 100644
index 000000000000..19b55f5039e4
--- /dev/null
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit cmake-utils
+
+MY_P="${PN}${PV}_src"
+
+DESCRIPTION="Fast, accurate chimera detection"
+HOMEPAGE="http://www.drive5.com/uchime/"
+SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+	cp "${FILESDIR}"/CMakeLists.txt . || die
+}