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

8 files changed, 455 insertions, 0 deletions

diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
new file mode 100644
index 000000000000..c3cf3842c604
--- /dev/null
+++ b/sci-biology/cd-hit/Manifest
@@ -0,0 +1,3 @@
+DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281
+DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 RMD160 00fca8d2527a4a6b1eda861f8f750e10ee565ae7 SHA1 743c4b6ec79b9d5acd1e1171587e96c03e3e3003 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a
+DIST cd-hit-v4.6-2012-04-25.tgz 652228 RMD160 318239a9416fd3cd57754546c8fcc0a4cea7f5d8 SHA1 e47c662c0a284ae99e47205d6a4eaea805a76cae SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9
diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
new file mode 100644
index 000000000000..d47948f0d821
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2011-01-31"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	emake ${myconf} || die
+}
+
+src_install() {
+	dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die
+	dodoc ChangeLog cdhit-user-guide.pdf || die
+}
diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
new file mode 100644
index 000000000000..bafa3301d724
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2011-03-07"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	emake ${myconf}
+}
+
+src_install() {
+	dodir /usr/bin
+	emake PREFIX="${ED}/usr/bin" install
+	dodoc ChangeLog cdhit-user-guide.pdf
+}
diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild
new file mode 100644
index 000000000000..d7dd15559c5c
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-04-25"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	emake ${myconf}
+}
+
+src_install() {
+	dodir /usr/bin
+	emake PREFIX="${ED}/usr/bin" install
+	dodoc ChangeLog
+	use doc && dodoc doc/*
+}
diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
new file mode 100644
index 000000000000..c3eaf79cc8f2
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
@@ -0,0 +1,85 @@
+diff --git a/Makefile b/Makefile
+index f1eaa26..92d3130 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -O2 -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,16 +18,16 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += -ggdb
+ endif
+ 
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++LDFLAGS += -o
+ 
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CXXFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -37,39 +37,39 @@ clean:
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+ 
diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
new file mode 100644
index 000000000000..5aa9b79e02ae
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
@@ -0,0 +1,98 @@
+ Makefile |   36 ++++++++++++++++++------------------
+ 1 files changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e8bac1d..bd31093 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -O2 -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,16 +18,16 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += -ggdb
+ endif
+ 
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++LDFLAGS += -o
+ 
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CXXFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -37,47 +37,47 @@ clean:
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+ 
+ PREFIX ?= /usr/local/bin
+ 
diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
new file mode 100644
index 000000000000..7a376eb8e73c
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.6-gentoo.patch
@@ -0,0 +1,117 @@
+ Makefile |   47 ++++++++++++++++++++++-------------------------
+ 1 files changed, 22 insertions(+), 25 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e9796a1..97dd72b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,16 +1,13 @@
+-
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++
+ 
+ # without OpenMP
+-CCFLAGS = -DNO_OPENMP
++#CXXFLAGS = -DNO_OPENMP
+ 
+ # with OpenMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,22 +15,22 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += 
+ else
+-CCFLAGS += -O2
++CXXFLAGS += 
+ endif
+ 
+ ifdef MAX_SEQ
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+ endif
+ 
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++#LDFLAGS += -o
+ 
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CXXFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -43,47 +40,47 @@ clean:
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+ 
+ PREFIX ?= /usr/local/bin
+ 
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
new file mode 100644
index 000000000000..bd5607ab16b5
--- /dev/null
+++ b/sci-biology/cd-hit/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+CD-HIT is a very widely used program for clustering and comparing large sets 
+of protein or nucleotide sequences. CD-HIT is very fast and can handle 
+extremely large databases. CD-HIT helps to significantly reduce the 
+computational and manual efforts in many sequence analysis tasks and aids in 
+understanding the data structure and correct the bias within a dataset.
+The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
+CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
+(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
+user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
+datasets and identifies the sequences in db2 that are similar to db1 above 
+a threshold. CD-HIT-454 is a program to identify natural and artificial 
+duplicates from pyrosequencing reads. The usage of other programs and 
+scripts can be found in CD-HIT user's guide.
+</longdescription>
+	<upstream>
+		<remote-id type="google-code">cdhit</remote-id>
+	</upstream>
+</pkgmetadata>