reinit the tree, so we can have metadata

4 files changed, 60 insertions, 0 deletions

diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
new file mode 100644
index 000000000000..8ff452aaf20e
--- /dev/null
+++ b/sci-biology/uchime/Manifest
@@ -0,0 +1,6 @@
+AUX CMakeLists.txt 549 SHA256 56ab311986a4ebf20dc8a0929d0ab1820233c0a81e7802b40ee683cf64895031 SHA512 02b43fbfa0a8fd9e5389033e5a8b97d356dfc2d29d076539eea5830b30526745014bc1eab302ccb8fd27b65a1afd92537b94c3c266a4b285de1b7a287fa8a867 WHIRLPOOL 8fa3739e15061160c78174c43f8b029ba46c1f892e3bc5686f4dca306f72bcbc3f96acfedb670db5c8b11ab642740e26f58860a83c148a7b8e1bc11927943016
+DIST uchime4.2.40_src.tar.gz 66772 SHA256 cb6a3aea4e8b4343a6e0ddde3b2755bbec53492bae5d6252ce8a7091061f353d SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b WHIRLPOOL 28ad19892ac8b4db03e93fd1fca39b05d6675c241a97f7a2ab241765589b34c56684ab4923eaf568a5f9b0e1583ce1460be7f0edf9d9201e5d3db3da0efb0ee6
+EBUILD uchime-4.2.40.ebuild 500 SHA256 b727045e5b473bb10d9af55201c54c4197937fa8358aa7521fecd0af249fd5ea SHA512 5e5757f0fb4de458662828805fc8b2d63573a450c7b6f5249f05103061f6f577ea91d7ec1fdea6889c3690647c536f79b35894e9d99040e12e111c2436b4c258 WHIRLPOOL dfaa621a4459ab7f873bd405ac7bf29e84a4591ce88005fac1a0136e4a78146c620a6e175d165c174e0faf1f55024059499818d777d0bf1dc3a1718a26cf93ed
+MISC ChangeLog 2632 SHA256 2e48d03b2b0907edd0bc919e11d69a7b631af489ba45be7e809ca79d3c3b5a3f SHA512 fd0d0ff3949449956cb3a283c6509913168470a8854595868bd8fb608e262bb858f4085fab84e29a6b73d6eaf9ce138142441b6403af29843afb7e8513bdab52 WHIRLPOOL ca525a6790d75da10a0a347aedf93be604ba6c38d6432bdb926490871eadb458c8e3915ca6ef69901508437a9f0332eceecca91686c84e2563a3063c77e78983
+MISC ChangeLog-2015 469 SHA256 616bb24f77f9c8e836e4752ee8f78c401dfd1e61127a94fdcab85c16747447e4 SHA512 f9cdd5ed5886021656d794f5299bafbd8719ea4b1c47dd2550df245827225f35613056923ea4f5ee33fe9add78ef2409be0ebbd0b953b86af75d89ee950314fa WHIRLPOOL df6ab45687bc4ed06d242530b3d0f325a6e3a1747f9a8b6bd66e76073ac38e699c9e98360292f4a3aa3c8817ecbdd07869d680fb355760da7ac1e4e593a67476
+MISC metadata.xml 896 SHA256 4952ea1a8c73ba8fa70e54b6e9f589efde2a9ffbb55d1cbab6199b954e875eb1 SHA512 641d91bff3651a49a3b7e15260cf2a758199ae49ece16643d3104f0f4e202938935edeb3bef18f7afc40a4eb1b1b3e469b07fec95d30a5e686e4b66535ff3e7e WHIRLPOOL 1994686e308ee6704205946dd8c3a7be908b941e21847d7098eac2f62ca2a511c3789f39a623950623fe54f15601217a8a3a5aacfaf36524ae4749e6cf0efa76
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 "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
+
+# Simply copy the source files from the mk script
+add_executable(uchime 
+				addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp)
+
+INSTALL(TARGETS uchime
+        DESTINATION bin)
diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml
new file mode 100644
index 000000000000..8e8ff4997171
--- /dev/null
+++ b/sci-biology/uchime/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<longdescription>
+UCHIME is a new algorithm for detecting chimeric sequences. It was developed in 
+collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob 
+Knight. Chimeras are commonly created during DNA sample amplification by 
+PCR, especially in community sequencing experiments using single regions 
+such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can 
+detect chimeras using a reference database or de novo using abundance 
+information on the assumption that chimeras are less abundant than their 
+parents because they must have undergone fewer rounds of amplification.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild
new file mode 100644
index 000000000000..dd2201547ae0
--- /dev/null
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+MY_P="${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
+
+	cmake-utils_src_prepare
+}