commit: 4004d49530eb309e24220d3998ed32edc592f381 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jun 1 18:19:23 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jun 1 18:19:23 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4004d495
sci-biology/cd-hit-4.6.1: version bump Package-Manager: portage-2.2.7 --- sci-biology/cd-hit/ChangeLog | 9 +++ sci-biology/cd-hit/cd-hit-4.6.1.ebuild | 44 +++++++++++ sci-biology/cd-hit/files/4.6.1-gentoo.patch | 118 ++++++++++++++++++++++++++++ sci-biology/cd-hit/metadata.xml | 23 ++++++ 4 files changed, 194 insertions(+) diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog new file mode 100644 index 0000000..2ef3e8f --- /dev/null +++ b/sci-biology/cd-hit/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/cd-hit +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cd-hit-4.6.1 (01 Jun 2014) + + 01 Jun 2014; Martin Mokrejs <[email protected]> + +cd-hit-4.6.1.ebuild, +files/4.6.1-gentoo.patch, +metadata.xml: + sci-biology/cd-hit-4.6.1: version bump diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild new file mode 100644 index 0000000..1c97d86 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2012-08-27" +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/4.6.1-gentoo.patch b/sci-biology/cd-hit/files/4.6.1-gentoo.patch new file mode 100644 index 0000000..d9db28c --- /dev/null +++ b/sci-biology/cd-hit/files/4.6.1-gentoo.patch @@ -0,0 +1,118 @@ +--- Makefile.ori 2014-06-01 20:12:44.000000000 +0200 ++++ Makefile 2014-06-01 20:16:34.000000000 +0200 +@@ -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 ($(openmp),yes) +-CCFLAGS = -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,17 +15,17 @@ + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(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 + +@@ -36,7 +33,7 @@ + CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS) + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -46,49 +43,49 @@ + # 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 ++PREFIX ?= $(DESTDIR)/usr/bin + + install: + for prog in $(PROGS); do \ diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml new file mode 100644 index 0000000..bd5607a --- /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>
